1
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Huang G, Song Z, Xu Y, Sun Y, Ding F. Deciphering the Morphological Difference of Amyloid-β Fibrils in Familial and Sporadic Alzheimer's Diseases. J Chem Inf Model 2024. [PMID: 39382320 DOI: 10.1021/acs.jcim.4c01471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
The aggregation of amyloid-β (Aβ) into amyloid fibrils is the major pathological hallmark of Alzheimer's disease (AD). Aβ fibrils can adopt a variety of morphologies, the relative populations of which are recently found to be associated with different AD subtypes such as familial and sporadic AD (fAD and sAD, respectively). The two AD subtypes differ in their ages of onset, AD-related genetic predispositions, and dominant Aβ fibril morphologies. We postulate that these disease subtype-dependent fibril morphology differences can be attributed to the intrinsic fibril properties and interacting molecules in the environment. Using atomistic discrete molecular dynamics simulations, we demonstrated that the fAD-dominant morphology exhibited a lower free-energy barrier for fibril growth but also a lower stability compared with the sAD-dominant fibril morphology, resulting in the time-dependent population change consistent with experimental observations. Additionally, we studied the effect of the Bri2 BRICHOS domain, an endogenous protein that has been reported to inhibit Aβ aggregation by preferential binding to fibrils, as one of the possible environmental factors. The Bri2 BRICHOS domain showed stronger binding to the fAD-dominant fibril than the sAD-dominant fibril in silico, suggesting a more effective suppression of fAD-dominant fibril formation. This result explains the high population of the sAD-dominant fibril morphology in sporadic cases with normal Bri2 functions. Genetic predisposition in fAD, on the other hand, might impair or overwhelm Bri2 functions, leading to a high population of fAD-associated fibril morphology. Together, our computational findings provide a theoretical framework for elucidating the AD subtypes entailed by distinct dominant amyloid fibril morphologies.
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Affiliation(s)
- Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Zhiyuan Song
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Yun Xu
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, United States
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2
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Lau D, Tang Y, Kenche V, Copie T, Kempe D, Jary E, Graves NJ, Biro M, Masters CL, Dzamko N, Gambin Y, Sierecki E. Single-Molecule Fingerprinting Reveals Different Growth Mechanisms in Seed Amplification Assays for Different Polymorphs of α-Synuclein Fibrils. ACS Chem Neurosci 2024; 15:3270-3285. [PMID: 39197832 PMCID: PMC11413846 DOI: 10.1021/acschemneuro.4c00185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 09/01/2024] Open
Abstract
α-Synuclein (αSyn) aggregates, detected in the biofluids of patients with Parkinson's disease (PD), have the ability to catalyze their own aggregation, leading to an increase in the number and size of aggregates. This self-templated amplification is used by newly developed assays to diagnose Parkinson's disease and turns the presence of αSyn aggregates into a biomarker of the disease. It has become evident that αSyn can form fibrils with slightly different structures, called "strains" or polymorphs, but little is known about their differential reactivity in diagnostic assays. Here, we compared the properties of two well-described αSyn polymorphs. Using single-molecule techniques, we observed that one of the polymorphs had an increased tendency to undergo secondary nucleation and we showed that this could explain the differences in reactivity observed in in vitro seed amplification assay and cellular assays. Simulations and high-resolution microscopy suggest that a 100-fold difference in the apparent rate of growth can be generated by a surprisingly low number of secondary nucleation "points" (1 every 2000 monomers added by elongation). When both strains are present in the same seeded reaction, secondary nucleation displaces proportions dramatically and causes a single strain to dominate the reaction as the major end product.
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Affiliation(s)
- Derrick Lau
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Yuan Tang
- Brain
and Mind Centre and Faculty of Medicine and Health, School of Medical
Sciences, University of Sydney, Camperdown, NSW 2050, Australia
| | - Vijaya Kenche
- Florey
Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Thomas Copie
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Daryan Kempe
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Eve Jary
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Noah J. Graves
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Maté Biro
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Colin L. Masters
- Florey
Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicolas Dzamko
- Brain
and Mind Centre and Faculty of Medicine and Health, School of Medical
Sciences, University of Sydney, Camperdown, NSW 2050, Australia
| | - Yann Gambin
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
| | - Emma Sierecki
- EMBL
Australia Node for Single Molecule Science and School of Biomedical
Sciences, Faculty of Medicine, The University
of New South Wales, Sydney, NSW 2052, Australia
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3
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Ahlawat S, Mehra S, Gowda CM, Maji SK, Agarwal V. Solid-state NMR assignment of α-synuclein polymorph prepared from helical intermediate. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10188-0. [PMID: 38963588 DOI: 10.1007/s12104-024-10188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/18/2024] [Indexed: 07/05/2024]
Abstract
Synucleinopathies are neurodegenerative diseases characterized by the accumulation of α-synuclein protein aggregates in the neurons and glial cells. Both ex vivo and in vitro α-synuclein fibrils tend to show polymorphism. Polymorphism results in structure variations among fibrils originating from a single polypeptide/protein. The polymorphs usually have different biophysical, biochemical and pathogenic properties. The various pathologies of a single disease might be associated with distinct polymorphs. Similarly, in the case of different synucleinopathies, each condition might be associated with a different polymorph. Fibril formation is a nucleation-dependent process involving the formation of transient and heterogeneous intermediates from monomers. Polymorphs are believed to arise from heterogeneous oligomer populations because of distinct selection mechanisms in different conditions. To test this hypothesis, we isolated and incubated different intermediates during in vitro fibrillization of α-synuclein to form different polymorphs. Here, we report 13C and 15N chemical shifts and the secondary structure of fibrils prepared from the helical intermediate using solid-state nuclear magnetic spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500 046, India.
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, India
| | - Chandrakala M Gowda
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500 046, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400 076, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, 500 046, India.
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4
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Toleikis Z, Paluch P, Kuc E, Petkus J, Sulskis D, Org-Tago ML, Samoson A, Smirnovas V, Stanek J, Lends A. Solid-state NMR backbone chemical shift assignments of α-synuclein amyloid fibrils at fast MAS regime. BIOMOLECULAR NMR ASSIGNMENTS 2024:10.1007/s12104-024-10186-2. [PMID: 38951472 DOI: 10.1007/s12104-024-10186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/18/2024] [Indexed: 07/03/2024]
Abstract
The α-synuclein (α-syn) amyloid fibrils are involved in various neurogenerative diseases. Solid-state NMR (ssNMR) has been showed as a powerful tool to study α-syn aggregates. Here, we report the 1H, 13C and 15N back-bone chemical shifts of a new α-syn polymorph obtained using proton-detected ssNMR spectroscopy under fast (95 kHz) magic-angle spinning conditions. The manual chemical shift assignments were cross-validated using FLYA algorithm. The secondary structural elements of α-syn fibrils were calculated using 13C chemical shift differences and TALOS software.
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Affiliation(s)
- Zigmantas Toleikis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, Vilnius, LT-10257, Lithuania
| | - Piotr Paluch
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Ewelina Kuc
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Jana Petkus
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Darius Sulskis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, Vilnius, LT-10257, Lithuania
| | - Mai-Liis Org-Tago
- Tallin University of Technology, Ehitajate tee 5, Tallinn, 19086, Estonia
| | - Ago Samoson
- Tallin University of Technology, Ehitajate tee 5, Tallinn, 19086, Estonia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, Vilnius, LT-10257, Lithuania
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Alons Lends
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia.
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5
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van der Wel PC. Solid-state nuclear magnetic resonance in the structural study of polyglutamine aggregation. Biochem Soc Trans 2024; 52:719-731. [PMID: 38563485 PMCID: PMC11088915 DOI: 10.1042/bst20230731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
The aggregation of proteins into amyloid-like fibrils is seen in many neurodegenerative diseases. Recent years have seen much progress in our understanding of these misfolded protein inclusions, thanks to advances in techniques such as solid-state nuclear magnetic resonance (ssNMR) spectroscopy and cryogenic electron microscopy (cryo-EM). However, multiple repeat-expansion-related disorders have presented special challenges to structural elucidation. This review discusses the special role of ssNMR analysis in the study of protein aggregates associated with CAG repeat expansion disorders. In these diseases, the misfolding and aggregation affect mutant proteins with expanded polyglutamine segments. The most common disorder, Huntington's disease (HD), is connected to the mutation of the huntingtin protein. Since the discovery of the genetic causes for HD in the 1990s, steady progress in our understanding of the role of protein aggregation has depended on the integrative and interdisciplinary use of multiple types of structural techniques. The heterogeneous and dynamic features of polyQ protein fibrils, and in particular those formed by huntingtin N-terminal fragments, have made these aggregates into challenging targets for structural analysis. ssNMR has offered unique insights into many aspects of these amyloid-like aggregates. These include the atomic-level structure of the polyglutamine core, but also measurements of dynamics and solvent accessibility of the non-core flanking domains of these fibrils' fuzzy coats. The obtained structural insights shed new light on pathogenic mechanisms behind this and other protein misfolding diseases.
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6
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Dhavale DD, Barclay AM, Borcik CG, Basore K, Berthold DA, Gordon IR, Liu J, Milchberg MH, O'Shea JY, Rau MJ, Smith Z, Sen S, Summers B, Smith J, Warmuth OA, Perrin RJ, Perlmutter JS, Chen Q, Fitzpatrick JAJ, Schwieters CD, Tajkhorshid E, Rienstra CM, Kotzbauer PT. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. Nat Commun 2024; 15:2750. [PMID: 38553463 PMCID: PMC10980826 DOI: 10.1038/s41467-024-46832-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. Here we develop and validate a method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and use solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise a mixture of single protofilament and two protofilament fibrils with very low twist. The protofilament fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural characterization of LBD Asyn fibrils and approaches for studying disease mechanisms, imaging agents and therapeutics targeting Asyn.
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Affiliation(s)
- Dhruva D Dhavale
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Alexander M Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Collin G Borcik
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine Basore
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Deborah A Berthold
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Isabelle R Gordon
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jialu Liu
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Moses H Milchberg
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jennifer Y O'Shea
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Zachary Smith
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Soumyo Sen
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brock Summers
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Owen A Warmuth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Richard J Perrin
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joel S Perlmutter
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Radiology, Neuroscience, Physical Therapy and Occupational Therapy, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - James A J Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Chad M Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Paul T Kotzbauer
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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7
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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] [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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8
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Mondal A, Dolui S, Dhabal S, Kundu S, Das L, Bhattacharjee A, Maiti NC. Structure specific neuro-toxicity of α-synuclein oligomer. Int J Biol Macromol 2023; 253:126683. [PMID: 37666396 DOI: 10.1016/j.ijbiomac.2023.126683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Parkinson's disease (PD) is linked to α-synuclein (aS) aggregation and deposition of amyloid in the substantia nigra region of the brain tissues. In the current investigation we produced two distinct classes of aS oligomer of differed protein conformation, stability and compared their toxic nature to cultured neuronal cells. Lyophilized oligomer (LO) was produced in storage of aS at-20 °C for 7 days and it was enriched with loosely hold molten globule like structure with residues having preferences for α-helical conformational space. The size of the oligomer was 4-5.5 nm under AFM. This kind of oligomer exhibited potential toxicity towards neuronal cell lines and did not transform into compact β-sheet rich amyloid fiber even after incubation at 37 °C for several days. Formation of another type of oligomer was often observed in the lag phase of aS fibrillation that often occurred at an elevated temperature (37 °C). This kind of heat induced oligomer (IO) was more hydrophobic and relatively less toxic to neuronal cells compared to lyophilized oligomer (LO). Importantly, initiation of hydrophobic zipping of aS caused the transformation of IO into thermodynamically stable β-sheet rich amyloid fibril. On the other hand, the presence of molten globule like conformation in LO, rendered greater toxicity to cultured neuronal cells.
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Affiliation(s)
- Animesh Mondal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Department of Zoology, Government General Degree College-Mangalkote, Purba Bardhaman, West Bengal 713132, India.
| | - Sandip Dolui
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Sukhamoy Dhabal
- Department of Biotechnology, National Institute of Technology-Durgapur, Mahatma Gandhi Rd, A-Zone, Durgapur, West Bengal 713209, India
| | - Shubham Kundu
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Lopamudra Das
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Ashish Bhattacharjee
- Department of Biotechnology, National Institute of Technology-Durgapur, Mahatma Gandhi Rd, A-Zone, Durgapur, West Bengal 713209, India
| | - Nakul C Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India.
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9
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Huang G, Tang H, Liu Y, Zhang C, Ke PC, Sun Y, Ding F. Direct Observation of Seeded Conformational Conversion of hIAPP In Silico Reveals the Mechanisms for Morphological Dependence and Asymmetry of Fibril Growth. J Chem Inf Model 2023; 63:5863-5873. [PMID: 37651616 PMCID: PMC10529695 DOI: 10.1021/acs.jcim.3c00898] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Rapid growth of amyloid fibrils via a seeded conformational conversion of monomers is a critical step of fibrillization and important for disease transmission and progression. Amyloid fibrils often display diverse morphologies with distinct populations, and yet the molecular mechanisms of fibril elongation and their corresponding morphological dependence remain poorly understood. Here, we computationally investigated the single-molecular growth of two experimentally resolved human islet amyloid polypeptide fibrils of different morphologies. In both cases, the incorporation of monomers into preformed fibrils was observed. The conformational conversion dynamics was characterized by a small number of fibril growth intermediates. Fibril morphology affected monomer binding at fibril elongation and lateral surfaces as well as the seeded conformational conversion dynamics at the fibril ends, resulting in different fibril elongation rates and populations. We also observed an asymmetric fibril growth as in our prior experiments, attributing to differences of two fibril ends in terms of their local surface curvatures and exposed hydrogen-bond donors and acceptors. Together, our mechanistic findings afforded a theoretical basis for delineating different amyloid strains-entailed divergent disease progression.
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Affiliation(s)
- Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Huayuan Tang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Chi Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Pu Chun Ke
- The Nanomedicine Center, The Great Bay Area National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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10
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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11
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Avni A, Joshi A, Mukhopadhyay S. Hydrogen-Deuterium Exchange Vibrational Raman Spectroscopy Distinguishes Distinct Amyloid Polymorphs Comprising Altered Core Architecture. J Phys Chem Lett 2023:5592-5601. [PMID: 37307286 DOI: 10.1021/acs.jpclett.3c01086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibrils are ordered protein aggregates comprising a hydrogen-bonded central cross-β core displaying a structural diversity in their supramolecular packing arrangements within the core. Such an altered packing results in amyloid polymorphism that gives rise to morphological and biological strain diversities. Here, we show that vibrational Raman spectroscopy coupled with hydrogen/deuterium (H/D) exchange discerns the key structural features that are responsible for yielding diverse amyloid polymorphs. Such a noninvasive and label-free methodology allows us to structurally distinguish distinct amyloid polymorphs displaying altered hydrogen bonding and supramolecular packing within the cross-β structural motif. By using quantitative molecular fingerprinting and multivariate statistical analysis, we analyze key Raman bands for the protein backbone and side chains that allow us to capture the conformational heterogeneity and structural distributions within distinct amyloid polymorphs. Our results delineate the key molecular factors governing the structural diversity in amyloid polymorphs and can potentially simplify studying amyloid remodeling by small molecules.
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12
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Dhavale DD, Barclay AM, Borcik CG, Basore K, Gordon IR, Liu J, Milchberg MH, O’shea J, Rau MJ, Smith Z, Sen S, Summers B, Smith J, Warmuth OA, Chen Q, Fitzpatrick JAJ, Schwieters CD, Tajkhorshid E, Rienstra CM, Kotzbauer PT. Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523303. [PMID: 36711931 PMCID: PMC9882085 DOI: 10.1101/2023.01.09.523303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. We developed and validated a novel method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and used solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise two protofilaments with pseudo-21 helical screw symmetry, very low twist and an interface formed by antiparallel beta strands of residues 85-93. The fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural landscape of LBD Asyn fibrils and inform further studies of disease mechanisms, imaging agents and therapeutics targeting Asyn.
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Affiliation(s)
- Dhruva D. Dhavale
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexander M. Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Collin G. Borcik
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine Basore
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Isabelle R. Gordon
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jialu Liu
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Moses H. Milchberg
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer O’shea
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J. Rau
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary Smith
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Soumyo Sen
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brock Summers
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Owen A. Warmuth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - James A. J. Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Charles D. Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53706 USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul T. Kotzbauer
- Department of Neurology and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
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13
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Bousset L, Alik A, Arteni A, Böckmann A, Meier BH, Melki R. α-Synuclein Fibril, Ribbon and Fibril-91 Amyloid Polymorphs Generation for Structural Studies. Methods Mol Biol 2023; 2551:345-355. [PMID: 36310214 DOI: 10.1007/978-1-0716-2597-2_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The human α-synuclein protein, identified as one of the main markers of Parkinson's disease, is a 140-amino acid thermostable protein that can easily be overexpressed in E. coli. The purification protocol determines the ability of the protein to assemble into amyloid fibrils of well-defined structures. Here, we describe the purification and assembly protocols to obtain three well-characterized amyloid forms (ribbon, fibrils, and fibril-91) used to assess their activity in biochemical and cellular assays or to investigate their atomic structure by cryo-electron microscopy and solid-state NMR.
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Affiliation(s)
- Luc Bousset
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France.
| | - Ania Alik
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Ana Arteni
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Ronald Melki
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
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14
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Meier BH, Böckmann A. Solid-State NMR Structure of Amyloid-β Fibrils. Methods Mol Biol 2023; 2551:53-62. [PMID: 36310196 DOI: 10.1007/978-1-0716-2597-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Amyloid fibrils are involved in a number of diseases and notably play a role in neurodegeneration, where they are present in plaques in the brain. Their structure determination might help in finding ways to interfere with their formation, and ultimately prevent disease, by revealing the structure-function relationship and helping to design molecules targeting initial assembly steps and further propagation. Here, we describe the different steps in NMR protocols which allowed the 3D structure determination of amyloid-β fibrils.
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Affiliation(s)
- Beat H Meier
- Physical Chemistry, ETH Zurich, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, Lyon, France.
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15
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Mehra S, Ahlawat S, Kumar H, Datta D, Navalkar A, Singh N, Patel K, Gadhe L, Kadu P, Kumar R, Jha NN, Sakunthala A, Sawner AS, Padinhateeri R, Udgaonkar JB, Agarwal V, Maji SK. α-Synuclein aggregation intermediates form fibril polymorphs with distinct prion-like properties. J Mol Biol 2022; 434:167761. [PMID: 35907572 DOI: 10.1016/j.jmb.2022.167761] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022]
Abstract
α-Synuclein (α-Syn) amyloids in synucleinopathies are suggested to be structurally and functionally diverse, reminiscent of prion-like strains. But how the aggregation of the same precursor protein results in the formation of fibril polymorphs remains elusive. Here, we demonstrate the structure-function relationship of two polymorphs, pre-matured fibrils (PMFs) and helix-matured fibrils (HMFs), based on α-Syn aggregation intermediates. These polymorphs display the structural differences as demonstrated by solid-state NMR and mass spectrometry studies and also possess different cellular activities such as seeding, internalization, and cell-to-cell transfer of aggregates. HMFs with a compact core structure exhibit low seeding potency but readily internalize and transfer from one cell to another. The less structured PMFs lack transcellular transfer ability but induce abundant α-Syn pathology and trigger the formation of aggresomes in cells. Overall, the study highlights that the conformational heterogeneity in the aggregation pathway may lead to fibril polymorphs with distinct prion-like behavior.
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Affiliation(s)
- Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Sahil Ahlawat
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad-500 046, India
| | - Harish Kumar
- Indian Institute of Science Education and Research, Pune- 411 008, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Nitu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Narendra N Jha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Arunima Sakunthala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Ajay S Sawner
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research, Pune- 411 008, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad-500 046, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India.
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16
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Quiñones-Ruiz T, Rosario-Alomar MF, Shanmugasundaram M, Ali MM, Lednev IK. Spontaneous Refolding of Amyloid Fibrils from One Polymorph to Another Caused by Changes in Environmental Hydrophobicity. Biochemistry 2022; 61:1456-1464. [PMID: 35786852 DOI: 10.1021/acs.biochem.2c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we report a new phenomenon in which lysozyme fibrils formed in a solution of acetic acid spontaneously refold to a different polymorph through a disassembled intermediate upon the removal of acetic acid. The structural changes were revealed and characterized by deep-UV resonance Raman spectroscopy, nonresonance Raman spectroscopy, intrinsic tryptophan fluorescence spectroscopy, and atomic force microscopy. A PPII-like structure with highly solvent-exposed tryptophan residues predominates the intermediate aggregates before refolding to polymorph II fibrils. Furthermore, the disulfide (SS) bonds undergo significant rearrangements upon the removal of acetic acid from the lysozyme fibril environment. The main SS bond conformation changes from gauche-gauche-trans in polymorph I to gauche-gauche-gauche in polymorph II. Changing the hydrophobicity of the fibril environment was concluded to be the decisive factor causing the spontaneous refolding of lysozyme fibrils from one polymorph to another upon the removal of acetic acid. Potential biological implications of the discovered phenomenon are discussed.
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Affiliation(s)
- Tatiana Quiñones-Ruiz
- Department of Chemistry, University at Albany, SUNY, Albany, New York 12222, United States
| | | | | | - Muhammad M Ali
- Department of Chemistry, University at Albany, SUNY, Albany, New York 12222, United States
| | - Igor K Lednev
- Department of Chemistry, University at Albany, SUNY, Albany, New York 12222, United States
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17
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Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy. Int J Mol Sci 2022; 23:ijms23126781. [PMID: 35743221 PMCID: PMC9224231 DOI: 10.3390/ijms23126781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/14/2022] Open
Abstract
S100A9 is a pro-inflammatory protein that co-aggregates with other proteins in amyloid fibril plaques. S100A9 can influence the aggregation kinetics and amyloid fibril structure of alpha-synuclein (α-syn), which is involved in Parkinson's disease. Currently, there are limited data regarding their cross-interaction and how it influences the aggregation process. In this work, we analyzed this interaction using solution 19F and 2D 15N-1H HSQC NMR spectroscopy and studied the aggregation properties of these two proteins. Here, we show that α-syn interacts with S100A9 at specific regions, which are also essential in the first step of aggregation. We also demonstrate that the 4-fluorophenylalanine label in alpha-synuclein is a sensitive probe to study interaction and aggregation using 19F NMR spectroscopy.
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18
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Chung CW, Stephens AD, Ward E, Feng Y, Davis MJ, Kaminski CF, Kaminski Schierle GS. Label-Free Characterization of Amyloids and Alpha-Synuclein Polymorphs by Exploiting Their Intrinsic Fluorescence Property. Anal Chem 2022; 94:5367-5374. [PMID: 35333515 PMCID: PMC8988127 DOI: 10.1021/acs.analchem.1c05651] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conventional in vitro aggregation assays often involve tagging with extrinsic fluorophores, which can interfere with aggregation. We propose the use of intrinsic amyloid fluorescence lifetime probed using two-photon excitation and represented by model-free phasor plots as a label-free assay to characterize the amyloid structure. Intrinsic amyloid fluorescence arises from the structured packing of β-sheets in amyloids and is independent of aromatic-based fluorescence. We show that different amyloids [i.e., α-Synuclein (αS), β-Lactoglobulin (βLG), and TasA] and different polymorphic populations of αS (induced by aggregation in salt-free and salt buffers mimicking the intra-/extracellular environments) can be differentiated by their unique fluorescence lifetimes. Moreover, we observe that disaggregation of the preformed fibrils of αS and βLG leads to increased fluorescence lifetimes, distinct from those of their fibrillar counterparts. Our assay presents a medium-throughput method for rapid classification of amyloids and their polymorphs (the latter of which recent studies have shown lead to different disease pathologies) and for testing small-molecule inhibitory compounds.
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Affiliation(s)
- Chyi Wei Chung
- Department of Chemical Engineering and Biotechnology, Phillipa Fawcett Drive, University of Cambridge, Cambridge, CB3 0AS, U.K
| | - Amberley D Stephens
- Department of Chemical Engineering and Biotechnology, Phillipa Fawcett Drive, University of Cambridge, Cambridge, CB3 0AS, U.K
| | - Edward Ward
- Department of Chemical Engineering and Biotechnology, Phillipa Fawcett Drive, University of Cambridge, Cambridge, CB3 0AS, U.K
| | - Yuqing Feng
- Department of Chemical Engineering and Biotechnology, Phillipa Fawcett Drive, University of Cambridge, Cambridge, CB3 0AS, U.K
| | - Molly Jo Davis
- Department of Chemical Engineering and Biotechnology, Phillipa Fawcett Drive, University of Cambridge, Cambridge, CB3 0AS, U.K
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, Phillipa Fawcett Drive, University of Cambridge, Cambridge, CB3 0AS, U.K
| | - Gabriele S Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, Phillipa Fawcett Drive, University of Cambridge, Cambridge, CB3 0AS, U.K
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19
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De Giorgi F, Abdul-Shukkoor MB, Kashyrina M, Largitte LA, De Nuccio F, Kauffmann B, Lends A, Laferrière F, Bonhommeau S, Lofrumento DD, Bousset L, Bezard E, Buffeteau T, Loquet A, Ichas F. Neurons with Cat's Eyes: A Synthetic Strain of α-Synuclein Fibrils Seeding Neuronal Intranuclear Inclusions. Biomolecules 2022; 12:436. [PMID: 35327628 PMCID: PMC8946814 DOI: 10.3390/biom12030436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 02/01/2023] Open
Abstract
The distinct neuropathological features of the different α-Synucleinopathies, as well as the diversity of the α-Synuclein (α-Syn) intracellular inclusion bodies observed in post mortem brain sections, are thought to reflect the strain diversity characterizing invasive α-Syn amyloids. However, this "one strain, one disease" view is still hypothetical, and to date, a possible disease-specific contribution of non-amyloid factors has not been ruled out. In Multiple System Atrophy (MSA), the buildup of α-Syn inclusions in oligodendrocytes seems to result from the terminal storage of α-Syn amyloid aggregates first pre-assembled in neurons. This assembly occurs at the level of neuronal cytoplasmic inclusions, and even earlier, within neuronal intranuclear inclusions (NIIs). Intriguingly, α-Syn NIIs are never observed in α-Synucleinopathies other than MSA, suggesting that these inclusions originate (i) from the unique molecular properties of the α-Syn fibril strains encountered in this disease, or alternatively, (ii) from other factors specifically dysregulated in MSA and driving the intranuclear fibrillization of α-Syn. We report the isolation and structural characterization of a synthetic human α-Syn fibril strain uniquely capable of seeding α-Syn fibrillization inside the nuclear compartment. In primary mouse cortical neurons, this strain provokes the buildup of NIIs with a remarkable morphology reminiscent of cat's eye marbles (see video abstract). These α-Syn inclusions form giant patterns made of one, two, or three lentiform beams that span the whole intranuclear volume, pushing apart the chromatin. The input fibrils are no longer detectable inside the NIIs, where they become dominated by the aggregation of endogenous α-Syn. In addition to its phosphorylation at S129, α-Syn forming the NIIs acquires an epitope antibody reactivity profile that indicates its organization into fibrils, and is associated with the classical markers of α-Syn pathology p62 and ubiquitin. NIIs are also observed in vivo after intracerebral injection of the fibril strain in mice. Our data thus show that the ability to seed NIIs is a strain property that is integrally encoded in the fibril supramolecular architecture. Upstream alterations of cellular mechanisms are not required. In contrast to the lentiform TDP-43 NIIs, which are observed in certain frontotemporal dementias and which are conditional upon GRN or VCP mutations, our data support the hypothesis that the presence of α-Syn NIIs in MSA is instead purely amyloid-strain-dependent.
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Affiliation(s)
- Francesca De Giorgi
- Institut des Maladies Neurodégénératives, CNRS, UMR 5293, 33076 Bordeaux, France; (L.-A.L.); (F.L.); (E.B.)
- Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, 33076 Bordeaux, France
| | - Muhammed Bilal Abdul-Shukkoor
- Institut de Chimie et de Biologie des Membranes et des Nano-objets, CNRS, UMR 5248, Université de Bordeaux, 33600 Pessac, France; (M.B.A.-S.); (A.L.); (A.L.)
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 33600 Pessac, France
| | - Marianna Kashyrina
- Department of Biological and Environmental Sciences and Technologies, Section of Human Anatomy, University of Salento, 73100 Lecce, Italy; (M.K.); (F.D.N.); (D.D.L.)
| | - Leslie-Ann Largitte
- Institut des Maladies Neurodégénératives, CNRS, UMR 5293, 33076 Bordeaux, France; (L.-A.L.); (F.L.); (E.B.)
- Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, 33076 Bordeaux, France
| | - Francesco De Nuccio
- Department of Biological and Environmental Sciences and Technologies, Section of Human Anatomy, University of Salento, 73100 Lecce, Italy; (M.K.); (F.D.N.); (D.D.L.)
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie, CNRS, Université de Bordeaux, INSERM, UMS3033/US001, 33600 Pessac, France;
| | - Alons Lends
- Institut de Chimie et de Biologie des Membranes et des Nano-objets, CNRS, UMR 5248, Université de Bordeaux, 33600 Pessac, France; (M.B.A.-S.); (A.L.); (A.L.)
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 33600 Pessac, France
| | - Florent Laferrière
- Institut des Maladies Neurodégénératives, CNRS, UMR 5293, 33076 Bordeaux, France; (L.-A.L.); (F.L.); (E.B.)
- Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, 33076 Bordeaux, France
| | - Sébastien Bonhommeau
- Institut des Sciences Moléculaires, CNRS, UMR 5255, Université de Bordeaux, 33400 Talence, France; (S.B.); (T.B.)
| | - Dario Domenico Lofrumento
- Department of Biological and Environmental Sciences and Technologies, Section of Human Anatomy, University of Salento, 73100 Lecce, Italy; (M.K.); (F.D.N.); (D.D.L.)
| | - Luc Bousset
- Laboratory of Neurodegenerative Diseases, Institut François Jacob, MIRCen, CEA, CNRS, 92265 Fontenay-aux-Roses, France;
| | - Erwan Bezard
- Institut des Maladies Neurodégénératives, CNRS, UMR 5293, 33076 Bordeaux, France; (L.-A.L.); (F.L.); (E.B.)
- Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, 33076 Bordeaux, France
| | - Thierry Buffeteau
- Institut des Sciences Moléculaires, CNRS, UMR 5255, Université de Bordeaux, 33400 Talence, France; (S.B.); (T.B.)
| | - Antoine Loquet
- Institut de Chimie et de Biologie des Membranes et des Nano-objets, CNRS, UMR 5248, Université de Bordeaux, 33600 Pessac, France; (M.B.A.-S.); (A.L.); (A.L.)
- Institut Européen de Chimie et Biologie, Université de Bordeaux, 33600 Pessac, France
| | - François Ichas
- Institut des Maladies Neurodégénératives, CNRS, UMR 5293, 33076 Bordeaux, France; (L.-A.L.); (F.L.); (E.B.)
- Institut des Maladies Neurodégénératives, UMR 5293, Université de Bordeaux, 33076 Bordeaux, France
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20
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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21
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Durell SR, Guy HR. The amyloid concentric β-barrel hypothesis: Models of synuclein oligomers, annular protofibrils, lipoproteins, and transmembrane channels. Proteins 2022; 90:512-542. [PMID: 34570382 PMCID: PMC8988847 DOI: 10.1002/prot.26249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/13/2021] [Indexed: 02/03/2023]
Abstract
Amyloid beta (Aβ of Alzheimer's disease) and α-synuclein (α-Syn of Parkinson's disease) form large fibrils. Evidence is increasing however that much smaller oligomers are more toxic and that these oligomers can form transmembrane ion channels. We have proposed previously that Aβ42 oligomers, annular protofibrils, and ion channels adopt concentric β-barrel molecular structures. Here we extend that hypothesis to the superfamily of α, β, and γ-synucleins. Our models of numerous synuclein oligomers, annular protofibrils, tubular protofibrils, lipoproteins, and ion channels were developed to be consistent with sizes, shapes, molecular weights, and secondary structures of assemblies as determined by electron microscopy and other studies. The models have the following features: (1) all subunits have identical structures and interactions; (2) they are consistent with conventional β-barrel theory; (3) the distance between walls of adjacent β-barrels is between 0.6 and 1.2 nm; (4) hydrogen bonds, salt bridges, interactions among aromatic side-chains, burial and tight packing of hydrophobic side-chains, and aqueous solvent exposure of hydrophilic side-chains are relatively optimal; and (5) residues that are identical among distantly related homologous proteins cluster in the interior of most oligomers whereas residues that are hypervariable are exposed on protein surfaces. Atomic scale models of some assemblies were developed.
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Affiliation(s)
- Stewart R Durell
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - H Robert Guy
- Amyloid Research Consultants (ARC), Cochiti Lake, New Mexico, USA
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22
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Alpha-Synuclein and Cognitive Decline in Parkinson Disease. Life (Basel) 2021; 11:life11111239. [PMID: 34833115 PMCID: PMC8625417 DOI: 10.3390/life11111239] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
Parkinson disease (PD) is the second most common neurodegenerative disorder in elderly people. It is characterized by the aggregation of misfolded alpha-synuclein throughout the nervous system. Aside from cardinal motor symptoms, cognitive impairment is one of the most disabling non-motor symptoms that occurs during the progression of the disease. The accumulation and spreading of alpha-synuclein pathology from the brainstem to limbic and neocortical structures is correlated with emerging cognitive decline in PD. This review summarizes the genetic and pathophysiologic relationship between alpha-synuclein and cognitive impairment in PD, together with potential areas of biomarker advancement.
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23
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Medeiros J, Bamm VV, Jany C, Coackley C, Ward ME, Harauz G, Ryan SD, Ladizhansky V. Partial magic angle spinning NMR 1H, 13C, 15N resonance assignments of the flexible regions of a monomeric alpha-synuclein: conformation of C-terminus in the lipid-bound and amyloid fibril states. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:297-303. [PMID: 33797711 DOI: 10.1007/s12104-021-10020-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Alpha-synuclein (α-syn) is a small presynaptic protein that is believed to play an important role in the pathogenesis of Parkinson's disease (PD). It localizes to presynaptic terminals where it partitions between a cytosolic soluble and a lipid-bound state. Recent evidence suggests that α-syn can also associate with mitochondrial membranes where it interacts with a unique anionic phospholipid cardiolipin (CL). Here, we examine the conformation of the flexible fragments of a monomeric α-syn bound to lipid vesicles composed of anionic 1,2-dioleoyl-sn-glycero-3-phosphate (DOPA) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipids, of tetraoleoyl CL (TOCL) and DOPC, and of fibrils. The dynamic properties of α-syn associated with DOPA:DOPC vesicles were the most favorable for conducting three-dimensional NMR experiments, and the 13C, 15N and amide 1H chemical shifts of the flexible and disordered C-terminus of α-syn could be assigned using three-dimensional through-bond magic angle spinning NMR spectroscopy. Although the C-terminus is more dynamically constrained in fibrils and in α-syn bound to TOCL:DOPC vesicles, a direct comparison of carbon chemical shifts detected using through bond two-dimensional spectroscopy indicates that the C-terminus is flexible and unstructured in all the three samples.
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Affiliation(s)
- Justin Medeiros
- Department of Physics, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Vladimir V Bamm
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Catherine Jany
- Department of Chemistry, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Carla Coackley
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Meaghan E Ward
- Department of Physics, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - George Harauz
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Scott D Ryan
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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24
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Han JY, Jang HS, Green AJE, Choi YP. RT-QuIC-based detection of alpha-synuclein seeding activity in brains of dementia with Lewy Body patients and of a transgenic mouse model of synucleinopathy. Prion 2021; 14:88-94. [PMID: 32041499 PMCID: PMC7039666 DOI: 10.1080/19336896.2020.1724608] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RT-QuIC is a shaking-based cyclic amplification technique originally developed in the prion field to detect minute amounts of scrapie prion protein (PrPSc). In this study, we applied the RT-QuIC assay to investigate a-synuclein (a-syn) seeding activity in brains of Dementia with Lewy Body (DLB) patients and in brains of G2-3 transgenic mice expressing human a-syn with A53T mutation. The results show that a-syn seeding activity varies between patients with detectable dilutions ranging from 10−3 to 10−8 dilutions of brain tissue and is stable under exposures to the cycles of freezing, thawing and sonication. A53T a-syn aggregates from G2-3 transgenic mice greatly favoured A53T recombinant human a-syn as substrates in comparison to wild-type a-syn, suggesting that conformations for wild-type a-syn to be able to adopt are not compatible with that of A53T aggregates from G2-3.
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Affiliation(s)
- Jung-Youn Han
- Laboratory Animal Center, Division of Research Strategy, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Hyung-Sup Jang
- Laboratory Animal Center, Division of Research Strategy, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Alison J E Green
- National CJD Research & Surveillance Unit, Centre for Clinical Brain Sciences, School of Clinical Sciences, University of Edinburgh, Edinburgh, UK
| | - Young Pyo Choi
- Laboratory Animal Center, Division of Research Strategy, Korea Brain Research Institute, Daegu, Republic of Korea
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25
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Mehra S, Gadhe L, Bera R, Sawner AS, Maji SK. Structural and Functional Insights into α-Synuclein Fibril Polymorphism. Biomolecules 2021; 11:1419. [PMID: 34680054 PMCID: PMC8533119 DOI: 10.3390/biom11101419] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Abnormal accumulation of aggregated α-synuclein (α-Syn) is seen in a variety of neurodegenerative diseases, including Parkinson's disease (PD), multiple system atrophy (MSA), dementia with Lewy body (DLB), Parkinson's disease dementia (PDD), and even subsets of Alzheimer's disease (AD) showing Lewy-body-like pathology. These synucleinopathies exhibit differences in their clinical and pathological representations, reminiscent of prion disorders. Emerging evidence suggests that α-Syn self-assembles and polymerizes into conformationally diverse polymorphs in vitro and in vivo, similar to prions. These α-Syn polymorphs arising from the same precursor protein may exhibit strain-specific biochemical properties and the ability to induce distinct pathological phenotypes upon their inoculation in animal models. In this review, we discuss clinical and pathological variability in synucleinopathies and several aspects of α-Syn fibril polymorphism, including the existence of high-resolution molecular structures and brain-derived strains. The current review sheds light on the recent advances in delineating the structure-pathogenic relationship of α-Syn and how diverse α-Syn molecular polymorphs contribute to the existing clinical heterogeneity in synucleinopathies.
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Affiliation(s)
- Surabhi Mehra
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (L.G.); (R.B.); (A.S.S.)
| | | | | | | | - Samir K. Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India; (L.G.); (R.B.); (A.S.S.)
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26
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Jan A, Gonçalves NP, Vaegter CB, Jensen PH, Ferreira N. The Prion-Like Spreading of Alpha-Synuclein in Parkinson's Disease: Update on Models and Hypotheses. Int J Mol Sci 2021; 22:8338. [PMID: 34361100 PMCID: PMC8347623 DOI: 10.3390/ijms22158338] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/11/2022] Open
Abstract
The pathological aggregation of the presynaptic protein α-synuclein (α-syn) and propagation through synaptically coupled neuroanatomical tracts is increasingly thought to underlie the pathophysiological progression of Parkinson's disease (PD) and related synucleinopathies. Although the precise molecular mechanisms responsible for the spreading of pathological α-syn accumulation in the CNS are not fully understood, growing evidence suggests that de novo α-syn misfolding and/or neuronal internalization of aggregated α-syn facilitates conformational templating of endogenous α-syn monomers in a mechanism reminiscent of prions. A refined understanding of the biochemical and cellular factors mediating the pathological neuron-to-neuron propagation of misfolded α-syn will potentially elucidate the etiology of PD and unravel novel targets for therapeutic intervention. Here, we discuss recent developments on the hypothesis regarding trans-synaptic propagation of α-syn pathology in the context of neuronal vulnerability and highlight the potential utility of novel experimental models of synucleinopathies.
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Affiliation(s)
- Asad Jan
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
| | - Nádia Pereira Gonçalves
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
- International Diabetic Neuropathy Consortium (IDNC), Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Christian Bjerggaard Vaegter
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
- International Diabetic Neuropathy Consortium (IDNC), Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Poul Henning Jensen
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
| | - Nelson Ferreira
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; (N.P.G.); (C.B.V.); (P.H.J.)
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27
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S100A9 Alters the Pathway of Alpha-Synuclein Amyloid Aggregation. Int J Mol Sci 2021; 22:ijms22157972. [PMID: 34360737 PMCID: PMC8348003 DOI: 10.3390/ijms22157972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
The formation of amyloid fibril plaques in the brain creates inflammation and neuron death. This process is observed in neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. Alpha-synuclein is the main protein found in neuronal inclusions of patients who have suffered from Parkinson's disease. S100A9 is a calcium-binding, pro-inflammation protein, which is also found in such amyloid plaques. To understand the influence of S100A9 on the aggregation of α-synuclein, we analyzed their co-aggregation kinetics and the resulting amyloid fibril structure by Fourier-transform infrared spectroscopy and atomic force microscopy. We found that the presence of S100A9 alters the aggregation kinetics of α-synuclein and stabilizes the formation of a particular amyloid fibril structure. We also show that the solution's ionic strength influences the interplay between S100A9 and α-synuclein, stabilizing a different structure of α-synuclein fibrils.
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28
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Mario Isas J, Pandey NK, Xu H, Teranishi K, Okada AK, Fultz EK, Rawat A, Applebaum A, Meier F, Chen J, Langen R, Siemer AB. Huntingtin fibrils with different toxicity, structure, and seeding potential can be interconverted. Nat Commun 2021; 12:4272. [PMID: 34257293 PMCID: PMC8277859 DOI: 10.1038/s41467-021-24411-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 06/17/2021] [Indexed: 11/09/2022] Open
Abstract
The first exon of the huntingtin protein (HTTex1) important in Huntington's disease (HD) can form cross-β fibrils of varying toxicity. We find that the difference between these fibrils is the degree of entanglement and dynamics of the C-terminal proline-rich domain (PRD) in a mechanism analogous to polyproline film formation. In contrast to fibril strains found for other cross-β fibrils, these HTTex1 fibril types can be interconverted. This is because the structure of their polyQ fibril core remains unchanged. Further, we find that more toxic fibrils of low entanglement have higher affinities for protein interactors and are more effective seeds for recombinant HTTex1 and HTTex1 in cells. Together these data show how the structure of a framing sequence at the surface of a fibril can modulate seeding, protein-protein interactions, and thereby toxicity in neurodegenerative disease.
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Affiliation(s)
- J Mario Isas
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nitin K Pandey
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hui Xu
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kazuki Teranishi
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alan K Okada
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Emergency Medicine, Regions Hospital, St. Paul, MN, USA
| | - Ellisa K Fultz
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anoop Rawat
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anise Applebaum
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Franziska Meier
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeannie Chen
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ralf Langen
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Ansgar B Siemer
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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29
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Murata T, Tochio N, Utsunomiya-Tate N. Physicochemical characterization of the G51D mutation of α-synuclein that is responsible for its severe cytotoxicity. Neurosci Lett 2021; 760:136077. [PMID: 34161822 DOI: 10.1016/j.neulet.2021.136077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/13/2021] [Indexed: 11/19/2022]
Abstract
Fibril formation and aggregation of α-synuclein are important for the pathogenesis of neurodegenerative disorders including Parkinson's disease. In familial Parkinson's disease, the G51D mutation of α-synuclein causes severe symptoms and rapid progression. α-Synuclein, an intrinsically disordered protein, was shown to adopt an α-helical tetrameric state that resists fibrillation and aggregation. Here, we isolated the stable dimeric state of recombinant wild-type (WT) α-synuclein and G51D α-synuclein protein. Using circular dichroism spectroscopy, we determined that the α-synuclein dimer and monomer structures were unfolded. The WT α-synuclein dimer was more resistant to fibril formation than the monomer. However, the fibril formation rate of the G51D α-synuclein dimer was similar to that of the G51D α-synuclein monomer. The fibril morphology and properties of the G51D α-synuclein monomer were different from those of the WT α-synuclein monomer and dimer and G51D α-synuclein dimer. Additionally, G51D α-synuclein monomer fibrils were more cytotoxic than other fibrils. Our findings indicate that the structural differences between G51D α-synuclein monomer fibrils and other fibrils are critically responsible for its severe neurotoxicity in familial Parkinson's disease.
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Affiliation(s)
- Takuya Murata
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Naoya Tochio
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo 173-8605, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo 173-8605, Japan.
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30
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Akbey Ü. Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H- 13C MAS NMR approach. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106974. [PMID: 33823335 DOI: 10.1016/j.jmr.2021.106974] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
We describe a 2H based MAS nuclear magnetic resonance (NMR) method to obtain site-specific molecular dynamics of biomolecules. The method utilizes the use of deuterium nucleus as a spin label that is proven to be very useful in dynamics studies of solid biological and functional materials. The aim is to understand overall characteristics of protein backbone and side-chain motions for CD3, CD2 and CD groups, in terms of timescale, type and activation energy of the underlying processes. Variable temperature two-dimensional (2D) 2H-13C correlation MAS NMR spectra were recorded for the uniformly 2H,13C,15N labelled Alanine and microcrystalline SH3 at a broad temperature range, from 320 K down to 100 K. First, the deuterium quadrupolar-coupling constant from specific D-C sites is obtained with the 2D experiment by utilizing carbon chemical shifts. Second, the static quadrupolar patterns are obtained at 100 K. Third, variable temperature approach enabled the observation of quadrupolar pattern over different motional regimes; slow, intermediate and fast. And finally, the apparent activation energies for C-D sites are determined and compared, by evaluating the temperature induced signal intensities. This information led to the determination of the dynamic processes for different D-C sites at a broad range of temperature and motional timescales. This is a first representation of 2D 2H-13C MAS NMR approach applied to fully isotope labelled deuterated protein covering 220 K temperature range.
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Affiliation(s)
- Ümit Akbey
- Weizmann Institute of Science, Department of Chemical and Biological Physics, Perlman Chemical Sciences Building, P.O. Box 26, Rehovot 76100, Israel.
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31
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Abstract
Protein aggregation is a widespread phenomenon with important implications in many scientific areas. Although amyloid formation is typically considered as detrimental, functional amyloids that perform physiological roles have been identified in all kingdoms of life. Despite their functional and pathological relevance, the structural details of the majority of molecular species involved in the amyloidogenic process remains elusive. Here, we explore the application of AlphaFold, a highly accurate protein structure predictor, in the field of protein aggregation. While we envision a straightforward application of AlphaFold in assisting the design of globular proteins with improved solubility for biomedical and industrial purposes, the use of this algorithm for predicting the structure of aggregated species seems far from trivial. First, in amyloid diseases, the presence of multiple amyloid polymorphs and the heterogeneity of aggregation intermediates challenges the "one sequence, one structure" paradigm, inherent to sequence-based predictions. Second, aberrant aggregation is not the subject of positive selective pressure, precluding the use of evolutionary-based approaches, which are the core of the AlphaFold pipeline. Instead, amyloid polymorphism seems to be constrained by the need for a defined structure-activity relationship in functional amyloids. They may thus provide a starting point for the application of AlphaFold in the amyloid landscape.
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32
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Hojjatian A, Dasari AKR, Sengupta U, Taylor D, Daneshparvar N, Yeganeh FA, Dillard L, Michael B, Griffin RG, Borgnia MJ, Kayed R, Taylor KA, Lim KH. Tau induces formation of α-synuclein filaments with distinct molecular conformations. Biochem Biophys Res Commun 2021; 554:145-150. [PMID: 33798940 PMCID: PMC8062303 DOI: 10.1016/j.bbrc.2021.03.091] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/17/2021] [Indexed: 11/17/2022]
Abstract
Recent structural investigation of amyloid filaments extracted from human patients demonstrated that the ex vivo filaments associated with different disease phenotypes adopt diverse molecular conformations, which are different from those of in vitro amyloid filaments. A very recent cryo-EM structural study also revealed that ex vivo α-synuclein filaments extracted from multiple system atrophy patients adopt distinct molecular structures from those of in vitro α-synuclein filaments, suggesting the presence of co-factors for α-synuclein aggregation in vivo. Here, we report structural characterizations of α-synuclein filaments formed in the presence of a potential co-factor, tau, using cryo-EM and solid-state NMR. Our cryo-EM structure of the tau-promoted α-synuclein filaments reveals some similarities to one of the previously reported polymorphs of in vitro α-synuclein filaments in the core region, while illustrating distinct conformations in the N- and C-terminal regions. The structural study highlights the conformational plasticity of α-synuclein filaments and the importance of the co-factors, requiring additional structural investigation of not only more ex vivo α-synuclein filaments, but also in vitro α-synuclein filaments formed in the presence of diverse co-factors. The comparative structural analyses will help better understand molecular basis of diverse structures of α-synuclein filaments and possible relevance of each structure to the disease phenotype.
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Affiliation(s)
- Alimohammad Hojjatian
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Urmi Sengupta
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Dianne Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Nadia Daneshparvar
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Fatemeh Abbasi Yeganeh
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Lucas Dillard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Brian Michael
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Rakez Kayed
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kenneth A Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4380, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA.
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33
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The differential solvent exposure of N-terminal residues provides "fingerprints" of alpha-synuclein fibrillar polymorphs. J Biol Chem 2021; 296:100737. [PMID: 33933456 PMCID: PMC8163981 DOI: 10.1016/j.jbc.2021.100737] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/15/2021] [Accepted: 04/28/2021] [Indexed: 01/13/2023] Open
Abstract
Synucleinopathies are neurodegenerative diseases characterized by the presence of intracellular deposits containing the protein alpha-synuclein (aSYN) within patients’ brains. It has been shown that aSYN can form structurally distinct fibrillar assemblies, also termed polymorphs. We previously showed that distinct aSYN polymorphs assembled in vitro, named fibrils, ribbons, and fibrils 91, differentially bind to and seed the aggregation of endogenous aSYN in neuronal cells, which suggests that distinct synucleinopathies may arise from aSYN polymorphs. In order to better understand the differential interactions of aSYN polymorphs with their partner proteins, we mapped aSYN polymorphs surfaces. We used limited proteolysis, hydrogen–deuterium exchange, and differential antibody accessibility to identify amino acids on their surfaces. We showed that the aSYN C-terminal region spanning residues 94 to 140 exhibited similarly high solvent accessibility in these three polymorphs. However, the N-terminal amino acid residues 1 to 38 of fibrils were exposed to the solvent, while only residues 1 to 18 within fibrils 91 were exposed, and no N-terminal residues within ribbons were solvent-exposed. It is likely that these differences in surface accessibility contribute to the differential binding of distinct aSYN polymorphs to partner proteins. We thus posit that the polypeptides exposed on the surface of distinct aSYN fibrillar polymorphs are comparable to fingerprints. Our findings have diagnostic and therapeutic potential, particularly in the prion-like propagation of fibrillar aSYN, as they can facilitate the design of ligands that specifically bind and distinguish between fibrillar polymorphs.
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Cascella R, Chen SW, Bigi A, Camino JD, Xu CK, Dobson CM, Chiti F, Cremades N, Cecchi C. The release of toxic oligomers from α-synuclein fibrils induces dysfunction in neuronal cells. Nat Commun 2021; 12:1814. [PMID: 33753734 PMCID: PMC7985515 DOI: 10.1038/s41467-021-21937-3] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
The self-assembly of α-synuclein (αS) into intraneuronal inclusion bodies is a key characteristic of Parkinson's disease. To define the nature of the species giving rise to neuronal damage, we have investigated the mechanism of action of the main αS populations that have been observed to form progressively during fibril growth. The αS fibrils release soluble prefibrillar oligomeric species with cross-β structure and solvent-exposed hydrophobic clusters. αS prefibrillar oligomers are efficient in crossing and permeabilize neuronal membranes, causing cellular insults. Short fibrils are more neurotoxic than long fibrils due to the higher proportion of fibrillar ends, resulting in a rapid release of oligomers. The kinetics of released αS oligomers match the observed kinetics of toxicity in cellular systems. In addition to previous evidence that αS fibrils can spread in different brain areas, our in vitro results reveal that αS fibrils can also release oligomeric species responsible for an immediate dysfunction of the neurons in the vicinity of these species.
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Affiliation(s)
- Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Serene W Chen
- Department of Life Science, Imperial College London, London, UK
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - José D Camino
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-Institute of Physical Chemistry "Rocasolano" (CSIC), University of Zaragoza, Zaragoza, Spain
| | - Catherine K Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-Institute of Physical Chemistry "Rocasolano" (CSIC), University of Zaragoza, Zaragoza, Spain.
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy.
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35
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Fibrilar Polymorphism of the Bacterial Extracellular Matrix Protein TasA. Microorganisms 2021; 9:microorganisms9030529. [PMID: 33806534 PMCID: PMC8000256 DOI: 10.3390/microorganisms9030529] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Functional amyloid proteins often appear as fibers in extracellular matrices of microbial soft colonies. In contrast to disease-related amyloid structures, they serve a functional goal that benefits the organism that secretes them, which is the reason for the title “functional”. Biofilms are a specific example of a microbial community in which functional amyloid fibers play a role. Functional amyloid proteins contribute to the mechanical stability of biofilms and mediate the adhesion of the cells to themselves as well as to surfaces. Recently, it has been shown that functional amyloid proteins also play a regulatory role in biofilm development. TasA is the major proteinaceous fibrilar component of the extracellular matrix of biofilms made of the soil bacterium and Gram-positive Bacillus subtilis. We have previously shown, as later corroborated by others, that in acidic solutions, TasA forms compact aggregates that are composed of tangled fibers. Here, we show that in a neutral pH and above a certain TasA concentration, the fibers of TasA are elongated and straight and that they bundle up in highly concentrated salt solutions. TasA fibers resemble the canonic amyloid morphology; however, these fibers also bear an interesting nm-scale periodicity along the fiber axis. At the molecular level, TasA fibers contain a twisted β-sheet structure, as indicated by circular dichroism measurements. Our study shows that the morphology of TasA fibers depends on the environmental conditions. Different fibrilar morphologies may be related with different functional roles in biofilms, ranging from granting biofilms with a mechanical support to acting as antibiotic agents.
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Scherpelz KP, Wang S, Pytel P, Madhurapantula RS, Srivastava AK, Sachleben JR, Orgel J, Ishii Y, Meredith SC. Atomic-level differences between brain parenchymal- and cerebrovascular-seeded Aβ fibrils. Sci Rep 2021; 11:247. [PMID: 33420184 PMCID: PMC7794565 DOI: 10.1038/s41598-020-80042-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 12/02/2020] [Indexed: 11/24/2022] Open
Abstract
Alzheimer's disease is characterized by neuritic plaques, the main protein components of which are β-amyloid (Aβ) peptides deposited as β-sheet-rich amyloid fibrils. Cerebral Amyloid Angiopathy (CAA) consists of cerebrovascular deposits of Aβ peptides; it usually accompanies Alzheimer's disease, though it sometimes occurs in the absence of neuritic plaques, as AD also occurs without accompanying CAA. Although neuritic plaques and vascular deposits have similar protein compositions, one of the characteristic features of amyloids is polymorphism, i.e., the ability of a single pure peptide to adopt multiple conformations in fibrils, depending on fibrillization conditions. For this reason, we asked whether the Aβ fibrils in neuritic plaques differed structurally from those in cerebral blood vessels. To address this question, we used seeding techniques, starting with amyloid-enriched material from either brain parenchyma or cerebral blood vessels (using meninges as the source). These amyloid-enriched preparations were then added to fresh, disaggregated solutions of Aβ to make replicate fibrils, as described elsewhere. Such fibrils were then studied by solid-state NMR, fiber X-ray diffraction, and other biophysical techniques. We observed chemical shift differences between parenchymal vs. vascular-seeded replicate fibrils in select sites (in particular, Ala2, Phe4, Val12, and Gln15 side chains) in two-dimensional 13C-13C correlation solid-state NMR spectra, strongly indicating structural differences at these sites. X-ray diffraction studies also indicated that vascular-seeded fibrils displayed greater order than parenchyma-seeded fibrils in the "side-chain dimension" (~ 10 Å reflection), though the "hydrogen-bond dimensions" (~ 5 Å reflection) were alike. These results indicate that the different nucleation conditions at two sites in the brain, parenchyma and blood vessels, affect the fibril products that get formed at each site, possibly leading to distinct pathophysiological outcomes.
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Affiliation(s)
| | - Songlin Wang
- Department of Chemistry, University of Illinois At Chicago, Chicago, IL, 60607, USA
| | - Peter Pytel
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Rama S Madhurapantula
- Department of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Atul K Srivastava
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph R Sachleben
- Biomolecular NMR Facility, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph Orgel
- Department of Biology and Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Stephen C Meredith
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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37
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Lacabanne D, Boudet J, Malär AA, Wu P, Cadalbert R, Salmon L, Allain FHT, Meier BH, Wiegand T. Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR. J Phys Chem B 2020; 124:11089-11097. [PMID: 33238710 PMCID: PMC7734624 DOI: 10.1021/acs.jpcb.0c08150] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Protein–nucleic
acid interactions are essential in a variety
of biological events ranging from the replication of genomic DNA to
the synthesis of proteins. Noncovalent interactions guide such molecular
recognition events, and protons are often at the center of them, particularly
due to their capability of forming hydrogen bonds to the nucleic acid
phosphate groups. Fast magic-angle spinning experiments (100 kHz)
reduce the proton NMR line width in solid-state NMR of fully protonated
protein–DNA complexes to such an extent that resolved proton
signals from side-chains coordinating the DNA can be detected. We
describe a set of NMR experiments focusing on the detection of protein
side-chains from lysine, arginine, and aromatic amino acids and discuss
the conclusions that can be obtained on their role in DNA coordination.
We studied the 39 kDa enzyme of the archaeal pRN1 primase complexed
with DNA and characterize protein–DNA contacts in the presence
and absence of bound ATP molecules.
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Affiliation(s)
| | - Julien Boudet
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Pengzhi Wu
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.,Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Loic Salmon
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.,Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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38
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Sorrentino ZA, Giasson BI. The emerging role of α-synuclein truncation in aggregation and disease. J Biol Chem 2020; 295:10224-10244. [PMID: 32424039 DOI: 10.1074/jbc.rev120.011743] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
α-Synuclein (αsyn) is an abundant brain neuronal protein that can misfold and polymerize to form toxic fibrils coalescing into pathologic inclusions in neurodegenerative diseases, including Parkinson's disease, Lewy body dementia, and multiple system atrophy. These fibrils may induce further αsyn misfolding and propagation of pathologic fibrils in a prion-like process. It is unclear why αsyn initially misfolds, but a growing body of literature suggests a critical role of partial proteolytic processing resulting in various truncations of the highly charged and flexible carboxyl-terminal region. This review aims to 1) summarize recent evidence that disease-specific proteolytic truncations of αsyn occur in Parkinson's disease, Lewy body dementia, and multiple system atrophy and animal disease models; 2) provide mechanistic insights on how truncation of the amino and carboxyl regions of αsyn may modulate the propensity of αsyn to pathologically misfold; 3) compare experiments evaluating the prion-like properties of truncated forms of αsyn in various models with implications for disease progression; 4) assess uniquely toxic properties imparted to αsyn upon truncation; and 5) discuss pathways through which truncated αsyn forms and therapies targeted to interrupt them. Cumulatively, it is evident that truncation of αsyn, particularly carboxyl truncation that can be augmented by dysfunctional proteostasis, dramatically potentiates the propensity of αsyn to pathologically misfold into uniquely toxic fibrils with modulated prion-like seeding activity. Therapeutic strategies and experimental paradigms should operate under the assumption that truncation of αsyn is likely occurring in both initial and progressive disease stages, and preventing truncation may be an effective preventative strategy against pathologic inclusion formation.
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Affiliation(s)
- Zachary A Sorrentino
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, Florida, USA.,Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Benoit I Giasson
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, Florida, USA .,Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, Florida, USA.,McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
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39
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Siemer AB. Advances in studying protein disorder with solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 106:101643. [PMID: 31972419 PMCID: PMC7202078 DOI: 10.1016/j.ssnmr.2020.101643] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/26/2023]
Abstract
Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Univeristy of Southern California, 1501 San Pablo Street, Los Angeles, CA, 90033, USA.
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40
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New insights on the structure of alpha-synuclein fibrils using cryo-electron microscopy. Curr Opin Neurobiol 2020; 61:89-95. [DOI: 10.1016/j.conb.2020.01.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 01/08/2023]
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41
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Cendrowska U, Silva PJ, Ait-Bouziad N, Müller M, Guven ZP, Vieweg S, Chiki A, Radamaker L, Kumar ST, Fändrich M, Tavanti F, Menziani MC, Alexander-Katz A, Stellacci F, Lashuel HA. Unraveling the complexity of amyloid polymorphism using gold nanoparticles and cryo-EM. Proc Natl Acad Sci U S A 2020; 117:6866-6874. [PMID: 32161130 PMCID: PMC7104366 DOI: 10.1073/pnas.1916176117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Increasing evidence suggests that amyloid polymorphism gives rise to different strains of amyloids with distinct toxicities and pathology-spreading properties. Validating this hypothesis is challenging due to a lack of tools and methods that allow for the direct characterization of amyloid polymorphism in hydrated and complex biological samples. Here, we report on the development of 11-mercapto-1-undecanesulfonate-coated gold nanoparticles (NPs) that efficiently label the edges of synthetic, recombinant, and native amyloid fibrils derived from different amyloidogenic proteins. We demonstrate that these NPs represent powerful tools for assessing amyloid morphological polymorphism, using cryogenic transmission electron microscopy (cryo-EM). The NPs allowed for the visualization of morphological features that are not directly observed using standard imaging techniques, including transmission electron microscopy with use of the negative stain or cryo-EM imaging. The use of these NPs to label native paired helical filaments (PHFs) from the postmortem brain of a patient with Alzheimer's disease, as well as amyloid fibrils extracted from the heart tissue of a patient suffering from systemic amyloid light-chain amyloidosis, revealed a high degree of homogeneity across the fibrils derived from human tissue in comparison with fibrils aggregated in vitro. These findings are consistent with, and strongly support, the emerging view that the physiologic milieu is a key determinant of amyloid fibril strains. Together, these advances should not only facilitate the profiling and characterization of amyloids for structural studies by cryo-EM, but also pave the way to elucidate the structural basis of amyloid strains and toxicity, and possibly the correlation between the pathological and clinical heterogeneity of amyloid diseases.
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Affiliation(s)
- Urszula Cendrowska
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Paulo Jacob Silva
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Nadine Ait-Bouziad
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Marie Müller
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Zekiye Pelin Guven
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sophie Vieweg
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Lynn Radamaker
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Senthil T Kumar
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081 Ulm, Germany
| | - Francesco Tavanti
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Francesco Stellacci
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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42
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Horváth D, Menyhárd DK, Perczel A. Protein Aggregation in a Nutshell: The Splendid Molecular Architecture of the Dreaded Amyloid Fibrils. Curr Protein Pept Sci 2020; 20:1077-1088. [PMID: 31553291 DOI: 10.2174/1389203720666190925102832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/04/2019] [Accepted: 04/07/2019] [Indexed: 11/22/2022]
Abstract
The recent high-resolution structures of amyloid fibrils show that the organization of peptide segments into amyloid aggregate architecture is a general process, though the morphology is more complex and intricate than suspected previously. The amyloid fibrils are often cytotoxic, accumulating as intracellular inclusions or extracellular plaques and have the ability to interfere with cellular physiology causing various cellular malfunctions. At the same time, the highly ordered amyloid structures also present an opportunity for nature to store and protect peptide chains under extreme conditions - something that might be used for designing storage, formulation, and delivery of protein medications or for contriving bio-similar materials of great resistance or structure-ordering capacity. Here we summarize amyloid characteristics; discussing the basic morphologies, sequential requirements and 3D-structure that are required for the understanding of this newly (re)discovered protein structure - a prerequisite for developing either inhibitors or promoters of amyloid-forming processes.
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Affiliation(s)
- Dániel Horváth
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
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43
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Lucas HR, Fernández RD. Navigating the dynamic landscape of alpha-synuclein morphology: a review of the physiologically relevant tetrameric conformation. Neural Regen Res 2020; 15:407-415. [PMID: 31571649 PMCID: PMC6921358 DOI: 10.4103/1673-5374.265792] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
N-acetylated α-synuclein (αSyn) has long been established as an intrinsically disordered protein associated with a dysfunctional role in Parkinson's disease. In recent years, a physiologically relevant, higher order conformation has been identified as a helical tetramer that is tailored by buried hydrophobic interactions and is distinctively aggregation resistant. The canonical mechanism by which the tetramer assembles remains elusive. As novel biochemical approaches, computational methods, pioneering purification platforms, and powerful imaging techniques continue to develop, puzzling information that once sparked debate as to the veracity of the tetramer has now shed light upon this new counterpart in αSyn neurobiology. Nuclear magnetic resonance and computational studies on multimeric αSyn structure have revealed that the protein folding propensity is controlled by small energy barriers that enable large scale reconfiguration. Alternatively, familial mutations ablate tetramerization and reconfigure polymorphic fibrillization. In this review, we will discuss the dynamic landscape of αSyn quaternary structure with a focus on the tetrameric conformation.
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Affiliation(s)
- Heather R Lucas
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Ricardo D Fernández
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
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44
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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45
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Rey NL, Bousset L, George S, Madaj Z, Meyerdirk L, Schulz E, Steiner JA, Melki R, Brundin P. α-Synuclein conformational strains spread, seed and target neuronal cells differentially after injection into the olfactory bulb. Acta Neuropathol Commun 2019; 7:221. [PMID: 31888771 PMCID: PMC6937797 DOI: 10.1186/s40478-019-0859-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022] Open
Abstract
Alpha-synuclein inclusions, the hallmarks of synucleinopathies, are suggested to spread along neuronal connections in a stereotypical pattern in the brains of patients. Ample evidence now supports that pathological forms of alpha-synuclein propagate in cell culture models and in vivo in a prion-like manner. However, it is still not known why the same pathological protein targets different cell populations, propagates with different kinetics and leads to a variety of diseases (synucleinopathies) with distinct clinical features. The aggregation of the protein alpha-synuclein yields different conformational polymorphs called strains. These strains exhibit distinct biochemical, physical and structural features they are able to imprint to newly recruited alpha-synuclein. This had led to the view that the clinical heterogeneity observed in synucleinopathies might be due to distinct pathological alpha-synuclein strains.To investigate the pathological effects of alpha-synuclein strains in vivo, we injected five different pure strains we generated de novo (fibrils, ribbons, fibrils-65, fibrils-91, fibrils-110) into the olfactory bulb of wild-type female mice. We demonstrate that they seed and propagate pathology throughout the olfactory network within the brain to different extents. We show strain-dependent inclusions formation in neurites or cell bodies. We detect thioflavin S-positive inclusions indicating the presence of mature amyloid aggregates.In conclusion, alpha-synuclein strains seed the aggregation of their cellular counterparts to different extents and spread differentially within the central nervous system yielding distinct propagation patterns. We provide here the proof-of-concept that the conformation adopted by alpha-synuclein assemblies determines their ability to amplify and propagate in the brain in vivo. Our observations support the view that alpha-synuclein polymorphs may underlie different propagation patterns within human brains.
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Affiliation(s)
- Nolwen L Rey
- Center for Neurodegenerative Science, Van Andel Institute, 333 Bostwick Avenue N.E, Grand Rapids, MI, 49503, USA.
- Institut François Jacob (MIRCen), CEA and Laboratory of Neurodegenerative diseases, UMR 9199 CNRS, 18 route du Panorama, 92265, Fontenay-aux-Roses, France.
| | - Luc Bousset
- Institut François Jacob (MIRCen), CEA and Laboratory of Neurodegenerative diseases, UMR 9199 CNRS, 18 route du Panorama, 92265, Fontenay-aux-Roses, France
| | - Sonia George
- Center for Neurodegenerative Science, Van Andel Institute, 333 Bostwick Avenue N.E, Grand Rapids, MI, 49503, USA
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, 333 Bostwick Avenue N.E, Grand Rapids, MI, 49503, USA
| | - Lindsay Meyerdirk
- Center for Neurodegenerative Science, Van Andel Institute, 333 Bostwick Avenue N.E, Grand Rapids, MI, 49503, USA
| | - Emily Schulz
- Center for Neurodegenerative Science, Van Andel Institute, 333 Bostwick Avenue N.E, Grand Rapids, MI, 49503, USA
| | - Jennifer A Steiner
- Center for Neurodegenerative Science, Van Andel Institute, 333 Bostwick Avenue N.E, Grand Rapids, MI, 49503, USA
| | - Ronald Melki
- Institut François Jacob (MIRCen), CEA and Laboratory of Neurodegenerative diseases, UMR 9199 CNRS, 18 route du Panorama, 92265, Fontenay-aux-Roses, France
| | - Patrik Brundin
- Center for Neurodegenerative Science, Van Andel Institute, 333 Bostwick Avenue N.E, Grand Rapids, MI, 49503, USA
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Guerrero-Ferreira R, Taylor NMI, Arteni AA, Kumari P, Mona D, Ringler P, Britschgi M, Lauer ME, Makky A, Verasdonck J, Riek R, Melki R, Meier BH, Böckmann A, Bousset L, Stahlberg H. Two new polymorphic structures of human full-length alpha-synuclein fibrils solved by cryo-electron microscopy. eLife 2019; 8:e48907. [PMID: 31815671 PMCID: PMC6957273 DOI: 10.7554/elife.48907] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/30/2019] [Indexed: 12/19/2022] Open
Abstract
Intracellular inclusions rich in alpha-synuclein are a hallmark of several neuropathological diseases including Parkinson's disease (PD). Previously, we reported the structure of alpha-synuclein fibrils (residues 1-121), composed of two protofibrils that are connected via a densely-packed interface formed by residues 50-57 (Guerrero-Ferreira, eLife 218;7:e36402). We here report two new polymorphic atomic structures of alpha-synuclein fibrils termed polymorphs 2a and 2b, at 3.0 Å and 3.4 Å resolution, respectively. These polymorphs show a radically different structure compared to previously reported polymorphs. The new structures have a 10 nm fibril diameter and are composed of two protofilaments which interact via intermolecular salt-bridges between amino acids K45, E57 (polymorph 2a) or E46 (polymorph 2b). The non-amyloid component (NAC) region of alpha-synuclein is fully buried by previously non-described interactions with the N-terminus. A hydrophobic cleft, the location of familial PD mutation sites, and the nature of the protofilament interface now invite to formulate hypotheses about fibril formation, growth and stability.
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Affiliation(s)
- Ricardo Guerrero-Ferreira
- Center for Cellular Imaging and NanoAnalytics (C-CINA), BiozentrumUniversity of BaselBaselSwitzerland
| | - Nicholas MI Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Ana-Andreea Arteni
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris Sud, Université Paris-SaclayGif-sur-YvetteFrance
- Institut Fancois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRSFontenay-Aux-RosesFrance
| | | | - Daniel Mona
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Medicine Area, Neuroscience DiscoveryRoche Innovation Center BaselBaselSwitzerland
| | - Philippe Ringler
- Center for Cellular Imaging and NanoAnalytics (C-CINA), BiozentrumUniversity of BaselBaselSwitzerland
| | - Markus Britschgi
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Medicine Area, Neuroscience DiscoveryRoche Innovation Center BaselBaselSwitzerland
| | - Matthias E Lauer
- Roche Pharma Research and Early Development, Therapeutic ModalitiesRoche Innovation Center BaselBaselSwitzerland
| | - Ali Makky
- Institut Galien Paris-Sud, CNRS, Université Paris-Sud, Université Paris-SaclayChâtenay-MalabryFrance
| | | | - Roland Riek
- Laboratory of Physical ChemistryETH ZurichZurichSwitzerland
| | - Ronald Melki
- Institut Fancois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRSFontenay-Aux-RosesFrance
| | - Beat H Meier
- Laboratory of Physical ChemistryETH ZurichZurichSwitzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural BiochemistryLabex Ecofect, UMR 5086 CNRS, Université de LyonLyonFrance
| | - Luc Bousset
- Institut Fancois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRSFontenay-Aux-RosesFrance
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), BiozentrumUniversity of BaselBaselSwitzerland
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de Oliveira GAP, Silva JL. Alpha-synuclein stepwise aggregation reveals features of an early onset mutation in Parkinson's disease. Commun Biol 2019; 2:374. [PMID: 31633065 PMCID: PMC6789109 DOI: 10.1038/s42003-019-0598-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/04/2019] [Indexed: 02/08/2023] Open
Abstract
Amyloid formation is a process involving interconverting protein species and results in toxic oligomers and fibrils. Aggregated alpha-synuclein (αS) participates in neurodegenerative maladies, but a closer understanding of the early αS polymerization stages and polymorphism of heritable αS variants is sparse still. Here, we distinguished αS oligomer and protofibril interconversions in Thioflavin T polymerization reactions. The results support a hypothesis reconciling the nucleation-polymerization and nucleation-conversion-polymerization models to explain the dissimilar behaviors of wild-type and the A53T mutant. Cryo-electron microscopy with a direct detector shows the polymorphic nature of αS fibrils formed by heritable A30P, E46K, and A53T point mutations. By showing that A53T rapidly nucleates competent species, continuously elongates fibrils in the presence of increasing amounts of seeds, and overcomes wild-type surface requirements for growth, our findings place A53T with features that may explain the early onset of familial Parkinson's disease cases bearing this mutation.
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Affiliation(s)
- Guilherme A. P. de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901 Brazil
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22904 USA
| | - Jerson L. Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901 Brazil
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48
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Lv G, Kumar A, Huang Y, Eliezer D. A Protofilament-Protofilament Interface in the Structure of Mouse α-Synuclein Fibrils. Biophys J 2019; 114:2811-2819. [PMID: 29925018 DOI: 10.1016/j.bpj.2018.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/11/2022] Open
Abstract
Fibrillar α-synuclein (AS) is the major component of Lewy bodies, the pathological hallmark of Parkinson's disease. Using solid-state nuclear magnetic resonance (ssNMR), we previously reported a structural characterization of mouse AS (mAS) fibrils and found that the secondary structure of the mAS fibrils is highly similar to a form of human AS (hAS) fibrils. Recently, a three-dimensional structure of these same hAS fibrils was determined by ssNMR and scanning transmission electron microscopy. Using medium- and long-range distance restraints obtained from ssNMR spectra, we found that the single protofilament structure of mAS fibrils is also similar to that of the hAS fibrils. However, residue-specific water accessibility of mAS fibrils probed by water polarization transfer ssNMR measurements indicates that residues S42-T44 and G84-V95 are largely protected from water even though they are located at the edge of the protofilament. Some of the corresponding resonances also exhibit peak doubling. These observations suggest that these residues may be involved in, to our knowledge, a novel protofilament-protofilament interface. We propose a structural model of mAS fibrils that incorporates this dimer interface.
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Affiliation(s)
- Guohua Lv
- Department of Biochemistry, Weill Cornell Medical College, New York, New York; Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, India; Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Yun Huang
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, New York.
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49
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Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 580] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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50
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Grozdanov V, Bousset L, Hoffmeister M, Bliederhaeuser C, Meier C, Madiona K, Pieri L, Kiechle M, McLean PJ, Kassubek J, Behrends C, Ludolph AC, Weishaupt JH, Melki R, Danzer KM. Increased Immune Activation by Pathologic α‐Synuclein in Parkinson's Disease. Ann Neurol 2019; 86:593-606. [DOI: 10.1002/ana.25557] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 01/01/2023]
Affiliation(s)
| | - Luc Bousset
- Molecular Imaging Research Center, Francois Jacob Institute, Alternative Energies and Atomic Energy Commission, and Laboratory of Neurodegenerative DiseasesNational Center for Scientific Research Fontenay‐Aux‐Roses France
| | - Meike Hoffmeister
- Institute of Biochemistry II, Medical SchoolGoethe University Frankfurt Germany
| | | | | | - Karine Madiona
- Molecular Imaging Research Center, Francois Jacob Institute, Alternative Energies and Atomic Energy Commission, and Laboratory of Neurodegenerative DiseasesNational Center for Scientific Research Fontenay‐Aux‐Roses France
| | - Laura Pieri
- Molecular Imaging Research Center, Francois Jacob Institute, Alternative Energies and Atomic Energy Commission, and Laboratory of Neurodegenerative DiseasesNational Center for Scientific Research Fontenay‐Aux‐Roses France
| | | | - Pamela J. McLean
- Department of NeuroscienceMayo Clinic Jacksonville Jacksonville FL
| | - Jan Kassubek
- Department of NeurologyUlm University Ulm Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Medical FacultyLudwig Maximilian University Munich Germany
| | | | | | - Ronald Melki
- Molecular Imaging Research Center, Francois Jacob Institute, Alternative Energies and Atomic Energy Commission, and Laboratory of Neurodegenerative DiseasesNational Center for Scientific Research Fontenay‐Aux‐Roses France
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