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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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Milardi D, Gazit E, Radford SE, Xu Y, Gallardo RU, Caflisch A, Westermark GT, Westermark P, Rosa CL, Ramamoorthy A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 2021; 121:1845-1893. [PMID: 33427465 DOI: 10.1021/acs.chemrev.0c00981] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.
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Affiliation(s)
- Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Gunilla T Westermark
- Department of Medical Cell Biology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 41809-1055, United States
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Neelamraju S, Wales DJ, Gosavi S. Protein energy landscape exploration with structure-based models. Curr Opin Struct Biol 2020; 64:145-151. [DOI: 10.1016/j.sbi.2020.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/30/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
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Especial J, Nunes A, Rey A, Faísca PF. Hydrophobic confinement modulates thermal stability and assists knotting in the folding of tangled proteins. Phys Chem Chem Phys 2019; 21:11764-11775. [PMID: 31114834 DOI: 10.1039/c9cp01701a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
There is growing support for the idea that the in vivo folding process of knotted proteins is assisted by chaperonins, but the mechanism of chaperonin assisted folding remains elusive. Here, we conduct extensive Monte Carlo simulations of lattice and off-lattice models to explore the effects of confinement and hydrophobic intermolecular interactions with the chaperonin cage in the folding and knotting processes. We find that moderate to high protein-cavity interactions (which are likely to be established in the beginning of the chaperonin working cycle) cause an energetic destabilization of the protein that overcomes the entropic stabilization driven by excluded volume, and leads to a decrease of the melting temperature relative to bulk conditions. Moreover, mild-to-moderate hydrophobic interactions with the cavity (which would be established later in the cycle) lead to a significant enhancement of knotting probability in relation to bulk conditions while simultaneously moderating the effect of steric confinement in the enhancement of thermal stability. Our results thus indicate that the chaperonin may be able to assist knotting without simultaneously thermally stabilizing potential misfolded states to a point that would hamper productive folding thus compromising its functional role.
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Affiliation(s)
- João Especial
- Departamento de Física, Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016 Lisboa, Portugal.
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Cheng Q, Joung I, Lee J, Kuwajima K, Lee J. Exploring the Folding Mechanism of Small Proteins GB1 and LB1. J Chem Theory Comput 2019; 15:3432-3449. [DOI: 10.1021/acs.jctc.8b01163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - InSuk Joung
- Department of Chemistry, Kangwon National University, Chuncheon 24341, South Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Juyong Lee
- Department of Chemistry, Kangwon National University, Chuncheon 24341, South Korea
| | - Kunihiro Kuwajima
- Department of Physics, University of Tokyo, Tokyo 113-0033, Japan
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Jooyoung Lee
- Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul 02455, South Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, South Korea
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