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Gilbert MAG, Fatima N, Jenkins J, O'Sullivan TJ, Schertel A, Halfon Y, Wilkinson M, Morrema THJ, Geibel M, Read RJ, Ranson NA, Radford SE, Hoozemans JJM, Frank RAW. CryoET of β-amyloid and tau within postmortem Alzheimer's disease brain. Nature 2024; 631:913-919. [PMID: 38987603 PMCID: PMC11269202 DOI: 10.1038/s41586-024-07680-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 06/06/2024] [Indexed: 07/12/2024]
Abstract
A defining pathological feature of most neurodegenerative diseases is the assembly of proteins into amyloid that form disease-specific structures1. In Alzheimer's disease, this is characterized by the deposition of β-amyloid and tau with disease-specific conformations. The in situ structure of amyloid in the human brain is unknown. Here, using cryo-fluorescence microscopy-targeted cryo-sectioning, cryo-focused ion beam-scanning electron microscopy lift-out and cryo-electron tomography, we determined in-tissue architectures of β-amyloid and tau pathology in a postmortem Alzheimer's disease donor brain. β-amyloid plaques contained a mixture of fibrils, some of which were branched, and protofilaments, arranged in parallel arrays and lattice-like structures. Extracellular vesicles and cuboidal particles defined the non-amyloid constituents of β-amyloid plaques. By contrast, tau inclusions formed parallel clusters of unbranched filaments. Subtomogram averaging a cluster of 136 tau filaments in a single tomogram revealed the polypeptide backbone conformation and filament polarity orientation of paired helical filaments within tissue. Filaments within most clusters were similar to each other, but were different between clusters, showing amyloid heterogeneity that is spatially organized by subcellular location. The in situ structural approaches outlined here for human donor tissues have applications to a broad range of neurodegenerative diseases.
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Affiliation(s)
- Madeleine A G Gilbert
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Nayab Fatima
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Joshua Jenkins
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Thomas J O'Sullivan
- Astbury Biostructure Laboratory CryoEM facility, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Andreas Schertel
- ZEISS Microscopy Customer Center Europe, Carl Zeiss Microscopy GmbH, Oberkochen, Germany
| | - Yehuda Halfon
- Astbury Biostructure Laboratory CryoEM facility, Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Tjado H J Morrema
- Department of Pathology, Unit Neuropathology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Mirjam Geibel
- ZEISS Microscopy Customer Center Europe, Carl Zeiss Microscopy GmbH, Oberkochen, Germany
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, 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
| | - Jeroen J M Hoozemans
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - René A W Frank
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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2
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Axell E, Hu J, Lindberg M, Dear AJ, Ortigosa-Pascual L, Andrzejewska EA, Šneiderienė G, Thacker D, Knowles TPJ, Sparr E, Linse S. The role of shear forces in primary and secondary nucleation of amyloid fibrils. Proc Natl Acad Sci U S A 2024; 121:e2322572121. [PMID: 38875148 PMCID: PMC11194593 DOI: 10.1073/pnas.2322572121] [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: 12/22/2023] [Accepted: 05/02/2024] [Indexed: 06/16/2024] Open
Abstract
Shear forces affect self-assembly processes ranging from crystallization to fiber formation. Here, the effect of mild agitation on amyloid fibril formation was explored for four peptides and investigated in detail for A[Formula: see text]42, which is associated with Alzheimer's disease. To gain mechanistic insights into the effect of mild agitation, nonseeded and seeded aggregation reactions were set up at various peptide concentrations with and without an inhibitor. First, an effect on fibril fragmentation was excluded by comparing the monomer-concentration dependence of aggregation kinetics under idle and agitated conditions. Second, using a secondary nucleation inhibitor, Brichos, the agitation effect on primary nucleation was decoupled from secondary nucleation. Third, an effect on secondary nucleation was established in the absence of inhibitor. Fourth, an effect on elongation was excluded by comparing the seeding potency of fibrils formed under idle or agitated conditions. We find that both primary and secondary nucleation steps are accelerated by gentle agitation. The increased shear forces facilitate both the detachment of newly formed aggregates from catalytic surfaces and the rate at which molecules are transported in the bulk solution to encounter nucleation sites on the fibril and other surfaces. Ultrastructural evidence obtained with cryogenic transmission electron microscopy and free-flow electrophoresis in microfluidics devices imply that agitation speeds up the detachment of nucleated species from the fibril surface. Our findings shed light on the aggregation mechanism and the role of detachment for efficient secondary nucleation. The results inform on how to modulate the relative importance of different microscopic steps in drug discovery and investigations.
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Affiliation(s)
- Emil Axell
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Jing Hu
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Max Lindberg
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Alexander J. Dear
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Lei Ortigosa-Pascual
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Ewa A. Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Greta Šneiderienė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Dev Thacker
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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3
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Raine J, Tolwinski N, Gruber J, Mathuru AS. Evaluating the inter-species transmission risk of amyloid beta peptide aggregates via ingestion. Alzheimers Res Ther 2024; 16:123. [PMID: 38849926 PMCID: PMC11157902 DOI: 10.1186/s13195-024-01487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 05/27/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND Recent reports suggest that amyloid beta (Aβ) peptides can exhibit prion-like pathogenic properties. Transmission of Aβ peptide and the development of associated pathologies after surgeries with contaminated instruments and intravenous or intracerebral inoculations have now been reported across fish, rodents, primates, and humans. This raises a worrying prospect of Aβ peptides also having other characteristics typical of prions, such as evasion of the digestive process. We asked if such transmission of Aβ aggregates via ingestion was possible. METHODS We made use of a transgenic Drosophila melanogaster line expressing human Aβ peptide prone to aggregation. Fly larvae were fed to adult zebrafish under two feeding schemes. The first was a short-term, high-intensity scheme over 48 h to determine transmission and retention in the gut. The second, long-term scheme specifically examined retention and accumulation in the brain. The gut and brain tissues were examined by histology, western blotting, and mass spectrometric analyses. RESULTS None of the analyses could detect Aβ aggregates in the guts of zebrafish following ingestion, despite being easily detectable in the feed. Additionally, there was no detectable accumulation of Aβ in the brain tissue or development of associated pathologies after prolonged feeding. CONCLUSIONS While human Aβ aggregates do not appear to be readily transmissible by ingestion across species, two prospects remain open. First, this mode of transmission, if occurring, may stay below a detectable threshold and may take much longer to manifest. A second possibility is that the human Aβ peptide is not able to trigger self-propagation or aggregation in other species. Either possibility requires further investigation, taking into account the possibility of such transmission from agricultural species used in the food industry.
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Affiliation(s)
- Joshua Raine
- Yale-NUS College, 12 College Avenue West, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nicholas Tolwinski
- Yale-NUS College, 12 College Avenue West, Singapore, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Jan Gruber
- Yale-NUS College, 12 College Avenue West, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ajay S Mathuru
- Yale-NUS College, 12 College Avenue West, Singapore, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Digital Medicine (WisDM) Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
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4
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Portugal Barron D, Guo Z. The supersaturation perspective on the amyloid hypothesis. Chem Sci 2023; 15:46-54. [PMID: 38131088 PMCID: PMC10731913 DOI: 10.1039/d3sc03981a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/27/2023] [Indexed: 12/23/2023] Open
Abstract
Development of therapeutic interventions for Alzheimer's over the past three decades has been guided by the amyloid hypothesis, which puts Aβ deposition as the initiating event of a pathogenic cascade leading to dementia. In the current form, the amyloid hypothesis lacks a comprehensive framework that considers the complex nature of Aβ aggregation. The explanation of how Aβ deposition leads to downstream pathology, and how reducing Aβ plaque load via anti-amyloid therapy can lead to improvement in cognition remains insufficient. In this perspective we integrate the concept of Aβ supersaturation into the amyloid hypothesis, laying out a framework for the mechanistic understanding and therapeutic intervention of Alzheimer's disease. We discuss the important distinction between in vitro and in vivo patterns of Aβ aggregation, the impact of different aggregation stages on therapeutic strategies, and how future investigations could integrate this concept in order to produce a more thorough understanding and better treatment for Alzheimer's and other amyloid-related disorders.
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Affiliation(s)
- Diana Portugal Barron
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer's Research and Care, David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer's Research and Care, David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
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5
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Lewkowicz E, Nakamura MN, Rynkiewicz MJ, Gursky O. Molecular modeling of apoE in complexes with Alzheimer's amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids. Cell Mol Life Sci 2023; 80:376. [PMID: 38010414 PMCID: PMC11061799 DOI: 10.1007/s00018-023-05026-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-β (Aβ) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aβ1-40 and Aβ1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aβ aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aβ aggregation.
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Affiliation(s)
- Emily Lewkowicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA
| | - Mari N Nakamura
- Undergraduate program, Department of Chemistry and Biochemistry, Middlebury College, 14 Old Chapel Rd, Middlebury, VT, 05753, USA
| | - Michael J Rynkiewicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA
| | - Olga Gursky
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, USA.
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6
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Lewkowicz E, Nakamura MN, Rynkiewicz MJ, Gursky O. Molecular modeling of apoE in complexes with Alzheimer's amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.551703. [PMID: 37577501 PMCID: PMC10418262 DOI: 10.1101/2023.08.04.551703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-β (Aβ) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aβ1-40 and Aβ1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aβ aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aβ aggregation.
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Affiliation(s)
- Emily Lewkowicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Mari N. Nakamura
- Undergraduate program, Department of Chemistry, Middlebury College, 14 Old Chapel Rd, Middlebury, VT 05753VT United States
| | - Michael J. Rynkiewicz
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
| | - Olga Gursky
- Department of Pharmacology, Physiology & Biophysics, Boston University Chobanian and Avedisian School of Medicine, W302, 700 Albany Street, Boston, MA, 02118, United States
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7
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Leistner C, Wilkinson M, Burgess A, Lovatt M, Goodbody S, Xu Y, Deuchars S, Radford SE, Ranson NA, Frank RAW. The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain. Nat Commun 2023; 14:2833. [PMID: 37198197 PMCID: PMC10192217 DOI: 10.1038/s41467-023-38495-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
Amyloid plaques composed of Aβ fibrils are a hallmark of Alzheimer's disease (AD). However, the molecular architecture of amyloid plaques in the context of fresh mammalian brain tissue is unknown. Here, using cryogenic correlated light and electron tomography we report the in situ molecular architecture of Aβ fibrils in the AppNL-G-F familial AD mouse model containing the Arctic mutation and an atomic model of ex vivo purified Arctic Aβ fibrils. We show that in-tissue Aβ fibrils are arranged in a lattice or parallel bundles, and are interdigitated by subcellular compartments, extracellular vesicles, extracellular droplets and extracellular multilamellar bodies. The Arctic Aβ fibril differs significantly from an earlier AppNL-F fibril structure, indicating a striking effect of the Arctic mutation. These structural data also revealed an ensemble of additional fibrillar species, including thin protofilament-like rods and branched fibrils. Together, these results provide a structural model for the dense network architecture that characterises β-amyloid plaque pathology.
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Affiliation(s)
- Conny Leistner
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ailidh Burgess
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Megan Lovatt
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Stanley Goodbody
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Susan Deuchars
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - René A W Frank
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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8
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Sun X, Dyson HJ, Wright PE. Role of conformational dynamics in pathogenic protein aggregation. Curr Opin Chem Biol 2023; 73:102280. [PMID: 36878172 PMCID: PMC10033434 DOI: 10.1016/j.cbpa.2023.102280] [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: 11/22/2022] [Revised: 01/13/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
The accumulation of pathogenic protein oligomers and aggregates is associated with several devastating amyloid diseases. As protein aggregation is a multi-step nucleation-dependent process beginning with unfolding or misfolding of the native state, it is important to understand how innate protein dynamics influence aggregation propensity. Kinetic intermediates composed of heterogeneous ensembles of oligomers are frequently formed on the aggregation pathway. Characterization of the structure and dynamics of these intermediates is critical to the understanding of amyloid diseases since oligomers appear to be the main cytotoxic agents. In this review, we highlight recent biophysical studies of the roles of protein dynamics in driving pathogenic protein aggregation, yielding new mechanistic insights that can be leveraged for design of aggregation inhibitors.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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9
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Ghosh S, Ali R, Verma S. Aβ-oligomers: A potential therapeutic target for Alzheimer's disease. Int J Biol Macromol 2023; 239:124231. [PMID: 36996958 DOI: 10.1016/j.ijbiomac.2023.124231] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
The cascade of amyloid formation relates to multiple complex events at the molecular level. Previous research has established amyloid plaque deposition as the leading cause of Alzheimer's disease (AD) pathogenesis, detected mainly in aged population. The primary components of the plaques are two alloforms of amyloid-beta (Aβ), Aβ1-42 and Aβ1-40 peptides. Recent studies have provided considerable evidence contrary to the previous claim indicating that amyloid-beta oligomers (AβOs) as the main culprit responsible for AD-associated neurotoxicity and pathogenesis. In this review, we have discussed the primary features of AβOs, such as assembly formation, the kinetics of oligomer formation, interactions with various membranes/membrane receptors, the origin of toxicity, and oligomer-specific detection methods. Recently, the discovery of rationally designed antibodies has opened a gateway for using synthesized peptides as a grafting component in the complementarity determining region (CDR) of antibodies. Thus, the Aβ sequence motif or the complementary peptide sequence in the opposite strand of the β-sheet (extracted from the Protein Data Bank: PDB) helps design oligomer-specific inhibitors. The microscopic event responsible for oligomer formation can be targeted, and thus prevention of the overall macroscopic behaviour of the aggregation or the associated toxicity can be achieved. We have carefully reviewed the oligomer formation kinetics and associated parameters. Besides, we have depicted a thorough understanding of how the synthesized peptide inhibitors can impede the early aggregates (oligomers), mature fibrils, monomers, or a mixture of the species. The oligomer-specific inhibitors (peptides or peptide fragments) lack in-depth chemical kinetics and optimization control-based screening. In the present review, we have proposed a hypothesis for effectively screening oligomer-specific inhibitors using the chemical kinetics (determining the kinetic parameters) and optimization control strategy (cost-dependent analysis). Further, it may be possible to implement the structure-kinetic-activity-relationship (SKAR) strategy instead of structure-activity-relationship (SAR) to improve the inhibitor's activity. The controlled optimization of the kinetic parameters and dose usage will be beneficial for narrowing the search window for the inhibitors.
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10
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Hutchison MT, Bellomo G, Cherepanov A, Stirnal E, Fürtig B, Richter C, Linhard V, Gurewitsch E, Lelli M, Morgner N, Schrader T, Schwalbe H. Modulation of Aβ42 Aggregation Kinetics and Pathway by Low-Molecular-Weight Inhibitors. Chembiochem 2023; 24:e202200760. [PMID: 36652672 DOI: 10.1002/cbic.202200760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
The aggregation of amyloid-β 42 (Aβ42) is directly related to the pathogenesis of Alzheimer's disease. Here, we have investigated the early stages of the aggregation process, during which most of the cytotoxic species are formed. Aβ42 aggregation kinetics, characterized by the quantification of Aβ42 monomer consumption, were tracked by real-time solution NMR spectroscopy (RT-NMR) allowing the impact that low-molecular-weight (LMW) inhibitors and modulators exert on the aggregation process to be analysed. Distinct differences in the Aβ42 kinetic profiles were apparent and were further investigated kinetically and structurally by using thioflavin T (ThT) and transmission electron microscopy (TEM), respectively. LMW inhibitors were shown to have a differential impact on early-state aggregation. Insight provided here could direct future therapeutic design based on kinetic profiling of the process of fibril formation.
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Affiliation(s)
- Marie-Theres Hutchison
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Giovanni Bellomo
- Laboratory of Clinical Neurochemistry Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy
| | - Alexey Cherepanov
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Elina Gurewitsch
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Moreno Lelli
- Chemistry Department, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM/CIRMMP), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Nina Morgner
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
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11
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Kutzli I, Zhou J, Li T, Baier SK, Mezzenga R. Formation and characterization of plant-based amyloid fibrils from hemp seed protein. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Abstract
The ability to detect and characterize multiple secondary structures or polymorphs within peptide and protein aggregates is crucial to treatment and prevention of amyloidogenic diseases, production of novel biomaterials, and many other applications. Here we report a label-free method to distinguish multiple β-sheet configurations within a single peptide aggregate using two-dimensional infrared spectroscopy. By calculating the transition dipole strength (TDS) spectrum from the ratio of linear and two-dimensional signals, we can extract maximum TDS values which provide higher sensitivity to vibrational coupling, and thus specifics of protein structure, than vibrational frequency alone. TDS spectra of AcKFE8 aggregates reveal two distinct β-sheet structures within fibers that appear homogeneous by other techniques. Furthermore, TDS spectra taken during early stages of aggregation show additional peaks that may indicate the presence of more weakly coupled β-sheet structures. These results demonstrate a unique and powerful spectroscopic method capable of distinguishing multiple oligomeric and polymorphic motifs throughout the aggregation using only native vibrational modes.
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Affiliation(s)
- William B Weeks
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lauren E Buchanan
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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13
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Sun X, Ferguson JA, Dyson HJ, Wright PE. A transthyretin monomer intermediate undergoes local unfolding and transient interaction with oligomers in a kinetically concerted aggregation pathway. J Biol Chem 2022; 298:102162. [PMID: 35724960 PMCID: PMC9293765 DOI: 10.1016/j.jbc.2022.102162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022] Open
Abstract
Transthyretin (TTR) amyloidosis is associated with tissue deposition of TTR aggregates. TTR aggregation is initiated by dissociation of the native tetramer to form a monomeric intermediate, which locally unfolds and assembles into soluble oligomers and higher-order aggregates. However, a detailed mechanistic understanding requires kinetic and structural characterization of the low-population intermediates formed. Here we show that the monomeric intermediate exchanges with an ensemble of oligomers on the millisecond timescale. This transient and reversible exchange causes broadening of the 19F resonance of a trifluoromethyl probe coupled to the monomeric intermediate at S85C. We show the 19F linewidth and R2 relaxation rate increase in a linear manner with increasing concentration of the oligomer. Furthermore, introduction of 19F probes at additional TTR sites yielded distinct 19F chemical shifts for the TTR tetramer and monomer when the trifluoromethyl probe was attached at S100C, located near the same subunit interface as S85C, but not with probes attached at S46C or E63C, which are distant from any interfaces. The 19F probe at E63C shows that part of the DE loop, which is solvent-accessible in the tetramer, becomes more buried in the NMR-visible oligomers. Finally, using backbone amides as probes, we show that parts of the EF helix and H strand become highly flexible in the otherwise structured monomeric intermediate at acidic pH. We further find that TTR aggregation can be reversed by increasing pH. Taken together, this work provides insights into location-dependent conformational changes in the reversible early steps of a kinetically-concerted TTR aggregation pathway.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - James A Ferguson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
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14
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Di Risola D, Ricci D, Marrocco I, Giamogante F, Grieco M, Francioso A, Vasco-Vidal A, Mancini P, Colotti G, Mosca L, Altieri F. ERp57 Chaperon Protein Protects Neuronal Cells from Aβ-induced toxicity. J Neurochem 2022; 162:322-336. [PMID: 35699375 PMCID: PMC9543391 DOI: 10.1111/jnc.15655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/21/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder whose main pathological hallmark is the accumulation of Amyloid-β peptide (Aβ) in the form of senile plaques. Aβ can cause neurodegeneration and disrupt cognitive functions by several mechanisms, including oxidative stress. ERp57 is a protein disulfide isomerase involved in the cellular stress response and known to be present in the cerebrospinal fluid of normal individuals as a complex with Aβ peptides, suggesting that it may be a carrier protein which prevents aggregation of Aβ. Although several studies show ERp57 involvement in neurodegenerative diseases, no clear mechanism of action has been identified thus far. In this work we gain insights into the interaction of Aβwith ERp57, with a special focus on the contribution of ERp57 to the defence system of the cell. Here we show that recombinant ERp57 directly interacts with the Aβ25-35 fragment in vitro with high affinityvia two in silico-predicted main sites of interaction. Furthermore, we used human neuroblastoma cells to show that short-term Aβ25-35 treatment induces ERp57 decrease in intracellular protein levels, different intracellular localization and ERp57 secretion in the cultured medium. Finally, we demonstrate that recombinant ERp57 counteracts the toxic effects of Aβ25-35 and restores cellular viability, by preventing Aβ25-35 aggregation. Overall, the present study shows thatextracellular ERp57 can exert a protective effect from Aβ toxicity and highlights it as a possible therapeutic tool in the treatment of AD.
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Affiliation(s)
- Daniel Di Risola
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy
| | - Daniela Ricci
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy.,Immunobiology of Infection Unit, Institut Pasteur, Paris, France
| | - Ilaria Marrocco
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Flavia Giamogante
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy.,Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Maddalena Grieco
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy
| | - Antonio Francioso
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy
| | - Aldrin Vasco-Vidal
- Leibniz Institute of Plant Biochemistry. Weinberg, Halle (Saale), Germany
| | - Patrizia Mancini
- Dept Experimental Medicine, Sapienza University of Roma, Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology - Italian National Research Council, Rome, Italy
| | - Luciana Mosca
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy
| | - Fabio Altieri
- Department of Biochemical Sciences, Sapienza University of Roma, Rome, Italy
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15
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Sampaio I, Quatroni FD, Pincela Lins PM, Nascimento AS, Zucolotto V. Modulation of beta-amyloid aggregation using ascorbic acid. Biochimie 2022; 200:36-43. [PMID: 35588896 DOI: 10.1016/j.biochi.2022.05.006] [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: 03/04/2022] [Revised: 04/18/2022] [Accepted: 05/11/2022] [Indexed: 12/11/2022]
Abstract
Studies have shown that the level of ascorbic acid (AA) is reduced in the brain of Alzheimer's disease (AD) patients. However, its effect on amyloid-β 1-42 (Aβ42) aggregation has not yet been elucidated. Here we investigated for the first time the effect of AA on Aβ42 aggregation using fluorescence assay, circular dichroism, atomic force microscopy, isothermal titration calorimetry, ligand docking, and molecular dynamics. Our results showed that the fibril content decreases in the growth phase when the peptides are co-incubated with AA. AA molecules bind to Aβ42 peptides with high binding affinity and a binding site for AA between the β-strands of Aβ42 oligomers prevents the stack of adjacent strands. We demonstrate the inhibitory effect of AA on the aggregation of Aβ42 and its molecular interactions, which can contribute to the development of an accessible therapy for AD and also to the design of novel drugs for other amyloidogenic diseases.
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Affiliation(s)
- Isabella Sampaio
- GNano - Nanomedicine and Nanotoxicology Group, Physics Institute of São Carlos, University of São Paulo, CP 369, 13560-970, São Carlos, SP, Brazil
| | - Felipe Domingues Quatroni
- GNano - Nanomedicine and Nanotoxicology Group, Physics Institute of São Carlos, University of São Paulo, CP 369, 13560-970, São Carlos, SP, Brazil
| | - Paula Maria Pincela Lins
- GNano - Nanomedicine and Nanotoxicology Group, Physics Institute of São Carlos, University of São Paulo, CP 369, 13560-970, São Carlos, SP, Brazil
| | - Alessandro S Nascimento
- Molecular Biotechnology Group, Physics Institute of São Carlos, University of São Paulo, CP 369, 13560-970, São Carlos, SP, Brazil
| | - Valtencir Zucolotto
- GNano - Nanomedicine and Nanotoxicology Group, Physics Institute of São Carlos, University of São Paulo, CP 369, 13560-970, São Carlos, SP, Brazil.
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16
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Watanabe-Nakayama T, Ono K. Single-molecule Observation of Self-Propagating Amyloid Fibrils. Microscopy (Oxf) 2022; 71:133-141. [DOI: 10.1093/jmicro/dfac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
The assembly of misfolded proteins into amyloid fibrils is associated with amyloidosis, including neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, and prion diseases. The self-propagation of amyloid fibrils is widely observed in the aggregation pathways of numerous amyloidogenic proteins. This propensity with plasticity in primary nucleation allows amyloid fibril polymorphism, which is correlated with the pathology/phenotypes of patients. Because the interference with the nucleation and replication processes of amyloid fibrils can alter the amyloid structure and the outcome of the disease, these processes can be a target for developing clinical drugs. Single-molecule observation of amyloid fibril replication can be an experimental system to provide the kinetic parameters for simulation studies and confirm the effect of clinical drugs. Here, we review single-molecule observation of the amyloid fibril replication process using fluorescence microscopy and time-lapse atomic force microscopy, including high-speed atomic force microscopy. We discussed the amyloid fibril replication process and combined single-molecule observation results with molecular dynamics simulations.
Mini Abstract Structural dynamics in amyloid aggregation is related with various Alzheimer’s and Parkinson’s disease symptoms. Single-molecule observation using high-speed atomic force microscopy can directly visualize the structural dynamics of individual amyloid aggregate assemblies. Here, we review historical and recent studies of single-molecule observation of amyloid aggregation with supportive molecular dynamics simulation.
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Affiliation(s)
| | - Kenjiro Ono
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa University, 13-1, Takara-machi, Kanazawa 920-8640, Japan
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17
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Meirovitch E, Liang Z, Freed JH. The N-Terminal Domain of Aβ 40-Amyloid Fibril: The MOMD Perspective of its Dynamic Structure from NMR Lineshape Analysis. J Phys Chem B 2022; 126:1202-1211. [PMID: 35128920 PMCID: PMC8908910 DOI: 10.1021/acs.jpcb.1c10131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed the stochastic microscopic-order-macroscopic-disorder (MOMD) approach for elucidating dynamic structures in the solid-state from 2H NMR lineshapes. In MOMD, the probe experiences an effective/collective motional mode. The latter is described by a potential, u, which represents the local spatial-restrictions, a local-motional diffusion tensor, R, and key features of local geometry. Previously we applied MOMD to the well-structured core domain of the 3-fold-symmetric twisted polymorph of the Aβ40-amyloid fibril. Here, we apply it to the N-terminal domain of this fibril. We find that the dynamic structures of the two domains are largely similar but differ in the magnitude and complexity of the key physical parameters. This interpretation differs from previous multisimple-mode (MSM) interpretations of the same experimental data. MSM used for the two domains different combinations of simple motional modes taken to be independent. For the core domain, MOMD and MSM disagree on the character of the dynamic structure. For the N-terminal domain, they even disagree on whether this chain segment is structurally ordered (MOMD finds that it is), and whether it undergoes a phase transition at 260 K where bulklike water located in the fibril matrix freezes (MOMD finds that it does not). These are major differences associated with an important system. While the MOMD description is a physically sound one, there are drawbacks in the MSM descriptions. The results obtained in this study promote our understanding of the dynamic structure of protein aggregates. Thus, they contribute to the effort to pharmacologically control neurodegenerative disorders believed to be caused by such aggregates.
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Affiliation(s)
- Eva Meirovitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zhichun Liang
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Jack H. Freed
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, United States
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18
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Hjalte J, Hossain S, Hugerth A, Sjögren H, Wahlgren M, Larsson P, Lundberg D. Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated by 1H NMR and All-Atom Molecular Dynamics Simulations. Mol Pharm 2022; 19:904-917. [PMID: 35104408 PMCID: PMC8905580 DOI: 10.1021/acs.molpharmaceut.1c00883] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding of peptide aggregation propensity is an important aspect in pharmaceutical development of peptide drugs. In this work, methodologies based on all-atom molecular dynamics (AA-MD) simulations and 1H NMR (in neat H2O) were evaluated as tools for identification and investigation of peptide aggregation. A series of structurally similar, pharmaceutically relevant peptides with known differences in aggregation behavior (D-Phe6-GnRH, ozarelix, cetrorelix, and degarelix) were investigated. The 1H NMR methodology was used to systematically investigate variations in aggregation with peptide concentration and time. Results show that 1H NMR can be used to detect the presence of coexisting classes of aggregates and the inclusion or exclusion of counterions in peptide aggregates. Interestingly, results suggest that the acetate counterions are included in aggregates of ozarelix and cetrorelix but not in aggregates of degarelix. The peptides investigated in AA-MD simulations (D-Phe6-GnRH, ozarelix, and cetrorelix) showed the same rank order of aggregation propensity as in the NMR experiments. The AA-MD simulations also provided molecular-level insights into aggregation dynamics, aggregation pathways, and the influence of different structural elements on peptide aggregation propensity and intermolecular interactions within the aggregates. Taken together, the findings from this study illustrate that 1H NMR and AA-MD simulations can be useful, complementary tools in early evaluation of aggregation propensity and formulation development for peptide drugs.
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Affiliation(s)
- Johanna Hjalte
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Shakhawath Hossain
- Department of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Andreas Hugerth
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Helen Sjögren
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Lund University, Box 124, 221 00 Lund, Sweden
| | - Per Larsson
- Department of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Dan Lundberg
- CR Competence AB, Center for Chemistry and Chemical Engineering, Box 124, 221 00 Lund, Sweden
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19
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Gouveia M, Sorčan T, Zemljič-Jokhadar Š, Travasso RDM, Liović M. A mathematical model for the dependence of keratin aggregate formation on the quantity of mutant keratin expressed in EGFP-K14 R125P keratinocytes. PLoS One 2021; 16:e0261227. [PMID: 34962936 PMCID: PMC8714116 DOI: 10.1371/journal.pone.0261227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
We examined keratin aggregate formation and the possible mechanisms involved. With this aim, we observed the effect that different ratios between mutant and wild-type keratins expressed in cultured keratinocytes may have on aggregate formation in vitro, as well as how keratin aggregate formation affects the mechanical properties of cells at the cell cortex. To this end we prepared clones with expression rates as close as possible to 25%, 50% and 100% of the EGFP-K14 proteins (either WT or R125P and V270M mutants). Our results showed that only in the case of the 25% EGFP-K14 R125P mutant significant differences could be seen. Namely, we observed in this case the largest accumulation of keratin aggregates and a significant reduction in cell stiffness. To gain insight into the possible mechanisms behind this observation, we extended our previous mathematical model of keratin dynamics by implementing a more complex reaction network that considers the coexistence of wild-type and mutant keratins in the cell. The new model, consisting of a set of coupled, non-linear, ordinary differential equations, allowed us to draw conclusions regarding the relative amounts of intermediate filaments and aggregates in cells, and suggested that aggregate formation by asymmetric binding between wild-type and mutant keratins could explain the data obtained on cells grown in culture.
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Affiliation(s)
- Marcos Gouveia
- Department of Physics, CFisUC, Center of Physics of the University of Coimbra, University of Coimbra, Coimbra, Portugal
- * E-mail: (MG); (RDMT); (ML)
| | | | - Špela Zemljič-Jokhadar
- Faculty of Medicine, Institute for Biophysics, University of Ljubljana, Ljubljana, Slovenia
| | - Rui D. M. Travasso
- Department of Physics, CFisUC, Center of Physics of the University of Coimbra, University of Coimbra, Coimbra, Portugal
- * E-mail: (MG); (RDMT); (ML)
| | - Mirjana Liović
- Faculty of Medicine, Medical Center for Molecular Biology, Institute for Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
- * E-mail: (MG); (RDMT); (ML)
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20
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Lattanzi V, André I, Gasser U, Dubackic M, Olsson U, Linse S. Amyloid β 42 fibril structure based on small-angle scattering. Proc Natl Acad Sci U S A 2021; 118:e2112783118. [PMID: 34815346 PMCID: PMC8640717 DOI: 10.1073/pnas.2112783118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Amyloid fibrils are associated with a number of neurodegenerative diseases, including fibrils of amyloid β42 peptide (Aβ42) in Alzheimer's disease. These fibrils are a source of toxicity to neuronal cells through surface-catalyzed generation of toxic oligomers. Detailed knowledge of the fibril structure may thus facilitate therapeutic development. We use small-angle scattering to provide information on the fibril cross-section dimension and shape for Aβ42 fibrils prepared in aqueous phosphate buffer at pH = 7.4 and pH 8.0 under quiescent conditions at 37 °C from pure recombinant Aβ42 peptide. Fitting the data using a continuum model reveals an elliptical cross-section and a peptide mass-per-unit length compatible with two filaments of two monomers, four monomers per plane. To provide a more detailed atomistic model, the data were fitted using as a starting state a high-resolution structure of the two-monomer arrangement in filaments from solid-state NMR (Protein Data Bank ID 5kk3). First, a twofold symmetric model including residues 11 to 42 of two monomers in the filament was optimized in terms of twist angle and local packing using Rosetta. A two-filament model was then built and optimized through fitting to the scattering data allowing the two N-termini in each filament to take different conformations, with the same conformation in each of the two filaments. This provides an atomistic model of the fibril with twofold rotation symmetry around the fibril axis. Intriguingly, no polydispersity as regards the number of filaments was observed in our system over separate samples, suggesting that the two-filament arrangement represents a free energy minimum for the Aβ42 fibril.
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Affiliation(s)
- Veronica Lattanzi
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden;
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ingemar André
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
| | - Urs Gasser
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Marija Dubackic
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Ulf Olsson
- Division of Physical Chemistry, Lund University, SE-22100 Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, SE-22100 Lund, Sweden
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21
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Andrade-Talavera Y, Chen G, Kurudenkandy FR, Johansson J, Fisahn A. Bri2 BRICHOS chaperone rescues impaired fast-spiking interneuron behavior and neuronal network dynamics in an AD mouse model in vitro. Neurobiol Dis 2021; 159:105514. [PMID: 34555537 DOI: 10.1016/j.nbd.2021.105514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022] Open
Abstract
Synchronized and properly balanced electrical activity of neurons is the basis for the brain's ability to process information, to learn, and to remember. In Alzheimer's disease (AD), which causes cognitive decline in patients, this synchronization and balance is disturbed by the accumulation of neuropathological biomarkers such as amyloid-beta peptide (Aβ42). Failure of Aβ42 clearance mechanisms as well as desynchronization of crucial neuronal classes such as fast-spiking interneurons (FSN) are root causes for the disruption of the cognition-relevant gamma brain rhythm (30-80 Hz) and consequent cognitive impairment observed in AD. Here we show that recombinant BRICHOS molecular chaperone domains from ProSP-C or Bri2, which interfere with Aβ42 aggregation, can rescue the gamma rhythm. We demonstrate that Aβ42 progressively decreases gamma oscillation power and rhythmicity, disrupts the inhibition/excitation balance in pyramidal cells, and desynchronizes FSN firing during gamma oscillations in the hippocampal CA3 network of mice. Application of the more efficacious Bri2 BRICHOS chaperone rescued the cellular and neuronal network performance from all ongoing Aβ42-induced functional impairments. Collectively, our findings offer critical missing data to explain the importance of FSN for normal network function and underscore the therapeutic potential of Bri2 BRICHOS to rescue the disruption of cognition-relevant brain rhythms in AD.
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Affiliation(s)
- Yuniesky Andrade-Talavera
- Neuronal Oscillations Laboratory, Division of Neurogeriatrics, Center for Alzheimer Research, Dept. of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17164 Solna, Sweden.
| | - Gefei Chen
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 141 57 Huddinge, Sweden; Department of Biosciences and Nutrition, Neo, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Firoz Roshan Kurudenkandy
- Neuronal Oscillations Laboratory, Division of Neurogeriatrics, Center for Alzheimer Research, Dept. of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17164 Solna, Sweden
| | - Jan Johansson
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 141 57 Huddinge, Sweden; Department of Biosciences and Nutrition, Neo, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - André Fisahn
- Neuronal Oscillations Laboratory, Division of Neurogeriatrics, Center for Alzheimer Research, Dept. of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17164 Solna, Sweden.
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22
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Zielinski M, Röder C, Schröder GF. Challenges in sample preparation and structure determination of amyloids by cryo-EM. J Biol Chem 2021; 297:100938. [PMID: 34224730 PMCID: PMC8335658 DOI: 10.1016/j.jbc.2021.100938] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/12/2023] Open
Abstract
Amyloids share a common architecture but play disparate biological roles in processes ranging from bacterial defense mechanisms to protein misfolding diseases. Their structures are highly polymorphic, which makes them difficult to study by X-ray diffraction or NMR spectroscopy. Our understanding of amyloid structures is due in large part to recent advances in the field of cryo-EM, which allows for determining the polymorphs separately. In this review, we highlight the main stepping stones leading to the substantial number of high-resolution amyloid fibril structures known today as well as recent developments regarding automation and software in cryo-EM. We discuss that sample preparation should move closer to physiological conditions to understand how amyloid aggregation and disease are linked. We further highlight new approaches to address heterogeneity and polymorphism of amyloid fibrils in EM image processing and give an outlook to the upcoming challenges in researching the structural biology of amyloids.
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Affiliation(s)
- Mara Zielinski
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Christine Röder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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23
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Toward the equilibrium and kinetics of amyloid peptide self-assembly. Curr Opin Struct Biol 2021; 70:87-98. [PMID: 34153659 DOI: 10.1016/j.sbi.2021.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/09/2021] [Accepted: 05/09/2021] [Indexed: 01/28/2023]
Abstract
Several devastating human diseases are linked to peptide self-assembly, but our understanding their onset and progression is not settled. This is a sign of the complexity of the aggregation process, which is prevented, catalyzed, or retarded by numerous factors in body fluids and cells, varying in time and space. Biophysical studies of pure peptide solutions contribute insights into the underlying steps in the process and quantitative parameters relating to rate constants (energy barriers) and equilibrium constants (population distributions). This requires methods to quantify the concentration of at least one species in the process. Translation to an in vivo situation poses an enormous challenge, and the effects of selected components (bottom up) or entire body fluids (top down) need to be quantified.
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24
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Meisl G, Kurt T, Condado-Morales I, Bett C, Sorce S, Nuvolone M, Michaels TCT, Heinzer D, Avar M, Cohen SIA, Hornemann S, Aguzzi A, Dobson CM, Sigurdson CJ, Knowles TPJ. Scaling analysis reveals the mechanism and rates of prion replication in vivo. Nat Struct Mol Biol 2021; 28:365-372. [PMID: 33767451 PMCID: PMC8922999 DOI: 10.1038/s41594-021-00565-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/26/2021] [Indexed: 01/03/2023]
Abstract
Prions consist of pathological aggregates of cellular prion protein and have the ability to replicate, causing neurodegenerative diseases, a phenomenon mirrored in many other diseases connected to protein aggregation, including Alzheimer's and Parkinson's diseases. However, despite their key importance in disease, the individual processes governing this formation of pathogenic aggregates, as well as their rates, have remained challenging to elucidate in vivo. Here we bring together a mathematical framework with kinetics of the accumulation of prions in mice and microfluidic measurements of aggregate size to dissect the overall aggregation reaction into its constituent processes and quantify the reaction rates in mice. Taken together, the data show that multiplication of prions in vivo is slower than in in vitro experiments, but efficient when compared with other amyloid systems, and displays scaling behavior characteristic of aggregate fragmentation. These results provide a framework for the determination of the mechanisms of disease-associated aggregation processes within living organisms.
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Affiliation(s)
- Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Timothy Kurt
- Department of Pathology, UC San Diego, San Diego, CA, USA
| | - Itzel Condado-Morales
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Cyrus Bett
- Department of Pathology, UC San Diego, San Diego, CA, USA
| | - Silvia Sorce
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Mario Nuvolone
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
- Amyloidosis Research and Treatment Center, Foundation IRCCS Policlinico San Matteo, Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Daniel Heinzer
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Merve Avar
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Samuel I A Cohen
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Wren Therapeutics, Cambridge, UK
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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25
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Leppert A, Tiiman A, Kronqvist N, Landreh M, Abelein A, Vukojević V, Johansson J. Smallest Secondary Nucleation Competent Aβ Aggregates Probed by an ATP-Independent Molecular Chaperone Domain. Biochemistry 2021; 60:678-688. [PMID: 33621049 PMCID: PMC8028046 DOI: 10.1021/acs.biochem.1c00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein oligomerization is a commonly encountered strategy by which the functional repertoire of proteins is increased. This, however, is a double-edged sword strategy because protein oligomerization is notoriously difficult to control. Living organisms have therefore developed a number of chaperones that prevent protein aggregation. The small ATP-independent molecular chaperone domain proSP-C BRICHOS, which is mainly trimeric, specifically inhibits fibril surface-catalyzed nucleation reactions that give rise to toxic oligomers during the aggregation of the Alzheimer's disease-related amyloid-β peptide (Aβ42). Here, we have created a stable proSP-C BRICHOS monomer mutant and show that it does not bind to monomeric Aβ42 but has a high affinity for Aβ42 fibrils, using surface plasmon resonance. Kinetic analysis of Aβ42 aggregation profiles, measured by thioflavin T fluorescence, reveals that the proSP-C BRICHOS monomer mutant strongly inhibits secondary nucleation reactions and thereby reduces the level of catalytic formation of toxic Aβ42 oligomers. To study binding between the proSP-C BRICHOS monomer mutant and small soluble Aβ42 aggregates, we analyzed fluorescence cross-correlation spectroscopy measurements with the maximum entropy method for fluorescence correlation spectroscopy. We found that the proSP-C BRICHOS monomer mutant binds to the smallest emerging Aβ42 aggregates that are comprised of eight or fewer Aβ42 molecules, which are already secondary nucleation competent. Our approach can be used to provide molecular-level insights into the mechanisms of action of substances that interfere with protein aggregation.
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Affiliation(s)
- Axel Leppert
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Ann Tiiman
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Axel Abelein
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Jan Johansson
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 14183 Huddinge, Sweden
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26
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Protofibril–Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Hasecke F, Niyangoda C, Borjas G, Pan J, Matthews G, Muschol M, Hoyer W. Protofibril-Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021; 60:3016-3021. [PMID: 33095508 PMCID: PMC7898819 DOI: 10.1002/anie.202010098] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/16/2020] [Indexed: 12/29/2022]
Abstract
Amyloid-β peptides (Aβ) assemble into both rigid amyloid fibrils and metastable oligomers termed AβO or protofibrils. In Alzheimer's disease, Aβ fibrils constitute the core of senile plaques, but Aβ protofibrils may represent the main toxic species. Aβ protofibrils accumulate at the exterior of senile plaques, yet the protofibril-fibril interplay is not well understood. Applying chemical kinetics and atomic force microscopy to the assembly of Aβ and lysozyme, protofibrils are observed to bind to the lateral surfaces of amyloid fibrils. When utilizing Aβ variants with different critical oligomer concentrations, the interaction inhibits the autocatalytic proliferation of amyloid fibrils by secondary nucleation on the fibril surface. Thus, metastable oligomers antagonize their replacement by amyloid fibrils both by competing for monomers and blocking secondary nucleation sites. The protofibril-fibril interaction governs their temporal evolution and potential to exert specific toxic activities.
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Affiliation(s)
- Filip Hasecke
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
| | | | - Gustavo Borjas
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Jianjun Pan
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | | | - Martin Muschol
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Wolfgang Hoyer
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
- Strukturbiochemie (IBI-7)Forschungszentrum Jülich52425JülichGermany
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28
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Lipiec E, Kaderli J, Kobierski J, Riek R, Skirlińska-Nosek K, Sofińska K, Szymoński M, Zenobi R. Nanoscale Hyperspectral Imaging of Amyloid Secondary Structures in Liquid. Angew Chem Int Ed Engl 2021; 60:4545-4550. [PMID: 32964527 DOI: 10.1002/anie.202010331] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 12/27/2022]
Abstract
Abnormal aggregation of amyloid-β is a very complex and heterogeneous process. Owing to methodological limitations, the aggregation pathway is still not fully understood. Herein a new approach is presented in which the secondary structure of single amyloid-β aggregates is investigated with tip-enhanced Raman spectroscopy (TERS) in a liquid environment. Clearly resolved TERS signatures of the amide I and amide III bands enabled a detailed analysis of the molecular structure of single aggregates at each phase of the primary aggregation of amyloid-β and also of small species on the surface of fibrils attributed to secondary nucleation. Notably, a β-sheet rearrangement from antiparallel in protofibrils to parallel in fibrils is observed. This study allows better understanding of Alzheimer's disease etiology and the methodology can be applied in studies of other neurodegenerative disorders.
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Affiliation(s)
- Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland.,Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.,The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Krakow, Poland
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Jan Kobierski
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy, Jagiellonian University Medical College, 31-007, Kraków, Poland
| | - Roland Riek
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | | | - Kamila Sofińska
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Marek Szymoński
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348, Kraków, Poland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
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29
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Lipiec E, Kaderli J, Kobierski J, Riek R, Skirlińska‐Nosek K, Sofińska K, Szymoński M, Zenobi R. Nanoscale Hyperspectral Imaging of Amyloid Secondary Structures in Liquid. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ewelina Lipiec
- M. Smoluchowski Institute of Physics Jagiellonian University Łojasiewicza 11 30-348 Kraków Poland
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics Polish Academy of Sciences 31-342 Krakow Poland
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Jan Kobierski
- Department of Pharmaceutical Biophysics Faculty of Pharmacy Jagiellonian University Medical College 31-007 Kraków Poland
| | - Roland Riek
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | | | - Kamila Sofińska
- M. Smoluchowski Institute of Physics Jagiellonian University Łojasiewicza 11 30-348 Kraków Poland
| | - Marek Szymoński
- M. Smoluchowski Institute of Physics Jagiellonian University Łojasiewicza 11 30-348 Kraków Poland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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30
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Chaplot K, Jarvela TS, Lindberg I. Secreted Chaperones in Neurodegeneration. Front Aging Neurosci 2020; 12:268. [PMID: 33192447 PMCID: PMC7481362 DOI: 10.3389/fnagi.2020.00268] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/03/2020] [Indexed: 12/11/2022] Open
Abstract
Protein homeostasis, or proteostasis, is a combination of cellular processes that govern protein quality control, namely, protein translation, folding, processing, and degradation. Disruptions in these processes can lead to protein misfolding and aggregation. Proteostatic disruption can lead to cellular changes such as endoplasmic reticulum or oxidative stress; organelle dysfunction; and, if continued, to cell death. A majority of neurodegenerative diseases involve the pathologic aggregation of proteins that subverts normal neuronal function. While prior reviews of neuronal proteostasis in neurodegenerative processes have focused on cytoplasmic chaperones, there is increasing evidence that chaperones secreted both by neurons and other brain cells in the extracellular - including transsynaptic - space play important roles in neuronal proteostasis. In this review, we will introduce various secreted chaperones involved in neurodegeneration. We begin with clusterin and discuss its identification in various protein aggregates, and the use of increased cerebrospinal fluid (CSF) clusterin as a potential biomarker and as a potential therapeutic. Our next secreted chaperone is progranulin; polymorphisms in this gene represent a known genetic risk factor for frontotemporal lobar degeneration, and progranulin overexpression has been found to be effective in reducing Alzheimer's- and Parkinson's-like neurodegenerative phenotypes in mouse models. We move on to BRICHOS domain-containing proteins, a family of proteins containing highly potent anti-amyloidogenic activity; we summarize studies describing the biochemical mechanisms by which recombinant BRICHOS protein might serve as a therapeutic agent. The next section of the review is devoted to the secreted chaperones 7B2 and proSAAS, small neuronal proteins which are packaged together with neuropeptides and released during synaptic activity. Since proteins can be secreted by both classical secretory and non-classical mechanisms, we also review the small heat shock proteins (sHsps) that can be secreted from the cytoplasm to the extracellular environment and provide evidence for their involvement in extracellular proteostasis and neuroprotection. Our goal in this review focusing on extracellular chaperones in neurodegenerative disease is to summarize the most recent literature relating to neurodegeneration for each secreted chaperone; to identify any common mechanisms; and to point out areas of similarity as well as differences between the secreted chaperones identified to date.
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Affiliation(s)
| | | | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
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31
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Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chem Sci 2020; 11:6236-6247. [PMID: 32953019 PMCID: PMC7480182 DOI: 10.1039/c9sc06501f] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation.
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Affiliation(s)
- Alexander J Dear
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Anđela Šarić
- Department of Physics and Astronomy , Institute for the Physics of Living Systems , University College London , Gower Street , London WC1E 6BT , UK
- MRC Laboratory for Molecular Cell Biology , University College London , Gower St, WC1E 6BT , London , UK
| | - Thomas C T Michaels
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , MA 02138 , USA
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics , Aarhus University , Høegh-Guldbergs Gade 6B , DK-8000 Aarhus C , Denmark
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Cavendish Laboratory , Department of Physics , University of Cambridge , J J Thomson Avenue , Cambridge CB3 0HE , UK .
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32
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Cerofolini L, Ravera E, Bologna S, Wiglenda T, Böddrich A, Purfürst B, Benilova I, Korsak M, Gallo G, Rizzo D, Gonnelli L, Fragai M, De Strooper B, Wanker EE, Luchinat C. Mixing Aβ(1–40) and Aβ(1–42) peptides generates unique amyloid fibrils. Chem Commun (Camb) 2020; 56:8830-8833. [DOI: 10.1039/d0cc02463e] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solid-state NMR experiments reveal that the two isoforms of the beta-amyloid peptide (Aβ(1–40) and Aβ(1–42)) are able to form unique interlaced mixed fibrils.
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