1
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Shen H, Liu K, Kong F, Ren M, Wang X, Wang S. Strategies for measuring concentrations and forms of amyloid-β peptides. Biosens Bioelectron 2024; 259:116405. [PMID: 38776801 DOI: 10.1016/j.bios.2024.116405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/01/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Alzheimer's disease (AD) is affecting more and more people worldwide without the effective treatment, while the existed pathological mechanism has been confirmed barely useful in the treatment. Amyloid-β peptide (Aβ), a main component of senile plaque, is regarded as the most promising target in AD treatment. Aβ clearance from AD brain seems to be a reliably therapeutic strategy, as the two exited drugs, GV-971 and aducanumab, are both developed based on it. However, doubt still exists. To exhaustive expound on the pathological mechanism of Aβ, rigorous analyses on the concentrations and aggregation forms are essential. Thus, it is attracting broad attention these years. However, most of the sensors have not been used in pathological studies, as the lack of the bridge between analytical chemist and pathologists. In this review, we made a brief introduce on Aβ-related pathological mechanism included in β-amyloid hypothesis to elucidate the detection conditions of sensor methods. Furthermore, a summary of the sensor methods was made, which were based on Aβ concentrations and form detections that have been developed in the past 10 years. As the greatest number of the sensors were built on fluorescent spectroscopy, electrochemistry, and Roman spectroscopy, detailed elucidation on them was made. Notably, the aggregation process is another important factor in revealing the progress of AD and developing the treatment methods, so the sensors on monitoring Aβ aggregation processes were also summarized.
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Affiliation(s)
- Hangyu Shen
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Keyin Liu
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Fangong Kong
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Mingguang Ren
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China
| | - Xiaoying Wang
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China; Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong, 264333, PR China.
| | - Shoujuan Wang
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250353, PR China.
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2
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Heath SG, Gray SG, Hamzah EM, O'Connor KM, Bozonet SM, Botha AD, de Cordovez P, Magon NJ, Naughton JD, Goldsmith DLW, Schwartfeger AJ, Sunde M, Buell AK, Morris VK, Göbl C. Amyloid formation and depolymerization of tumor suppressor p16 INK4a are regulated by a thiol-dependent redox mechanism. Nat Commun 2024; 15:5535. [PMID: 38951545 PMCID: PMC11217399 DOI: 10.1038/s41467-024-49581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
The conversion of a soluble protein into polymeric amyloid structures is a process that is poorly understood. Here, we describe a fully redox-regulated amyloid system in which cysteine oxidation of the tumor suppressor protein p16INK4a leads to rapid amyloid formation. We identify a partially-structured disulfide-bonded dimeric intermediate species that subsequently assembles into fibrils. The stable amyloid structures disassemble when the disulfide bond is reduced. p16INK4a is frequently mutated in cancers and is considered highly vulnerable to single-point mutations. We find that multiple cancer-related mutations show increased amyloid formation propensity whereas mutations stabilizing the fold prevent transition into amyloid. The complex transition into amyloids and their structural stability is therefore strictly governed by redox reactions and a single regulatory disulfide bond.
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Affiliation(s)
- Sarah G Heath
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Shelby G Gray
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emilie M Hamzah
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Karina M O'Connor
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Stephanie M Bozonet
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Alex D Botha
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Pierre de Cordovez
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Nicholas J Magon
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Jennifer D Naughton
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Dylan L W Goldsmith
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, Sydney, Australia
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Vanessa K Morris
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
| | - Christoph Göbl
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
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3
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Dormann D, Lemke EA. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 2024; 26:851-858. [PMID: 38783141 DOI: 10.1038/s41556-024-01423-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
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Affiliation(s)
- Dorothee Dormann
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
| | - Edward Anton Lemke
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg University, Mainz, Germany.
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4
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Balana AT, Mahul-Mellier AL, Nguyen BA, Horvath M, Javed A, Hard ER, Jasiqi Y, Singh P, Afrin S, Pedretti R, Singh V, Lee VMY, Luk KC, Saelices L, Lashuel HA, Pratt MR. O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology. Nat Chem Biol 2024; 20:646-655. [PMID: 38347213 PMCID: PMC11062923 DOI: 10.1038/s41589-024-01551-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024]
Abstract
Amyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer's and Parkinson's disease, can form different fibril structures or strains with distinct toxic properties, seeding activities and pathology. Understanding the determinants contributing to the formation of different amyloid features could open new avenues for developing disease-specific diagnostics and therapies. Here we report that O-GlcNAc modification of α-synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by cryogenic electron microscopy, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinson's disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc-modified fibrils remain unclear, our in vitro mechanistic studies indicate that heat shock proteins interactions with O-GlcNAc fibril inhibit their seeding activity, suggesting that the O-GlcNAc modification may alter the interactome of the α-synuclein fibrils in ways that lead to reduce seeding activity in vivo. Our results show that posttranslational modifications, such as O-GlcNAc modification, of α-synuclein are key determinants of α-synuclein amyloid strains and pathogenicity.
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Affiliation(s)
- Aaron T Balana
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Anne-Laure Mahul-Mellier
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Binh A Nguyen
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mian Horvath
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Afraah Javed
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Eldon R Hard
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yllza Jasiqi
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Preeti Singh
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Shumaila Afrin
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rose Pedretti
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Virender Singh
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Virginia M-Y Lee
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelvin C Luk
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lorena Saelices
- Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
- Department Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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5
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Santos J, Pallarès I, Ventura S. A glimpse into the structural properties of α-synuclein oligomers. Biofactors 2024; 50:439-449. [PMID: 38063360 DOI: 10.1002/biof.2021] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/03/2023] [Indexed: 06/15/2024]
Abstract
α-Synuclein (αS) aggregation is the main neurological hallmark of a group of debilitating neurodegenerative disorders, collectively referred to as synucleinopathies, of which Parkinson's disease is the most prevalent. αS oligomers formed during the initial stages of aggregation are considered key pathogenic drivers of disease onset and progression, standing as privileged targets for therapeutic intervention and diagnosis. However, the structure of αS oligomers and the mechanistic basis of oligomer to fibril conversion are yet poorly understood, thereby precluding the rational formulation of strategies aimed at targeting oligomeric species. In this review, we delve into the recent advances in the structural and mechanistic characterization of αS oligomers. We also discuss how these advances are transforming our understanding of these elusive species and paving the way for oligomer-targeting therapeutics and diagnosis.
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Affiliation(s)
- Jaime Santos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irantzu Pallarès
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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6
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Chitty C, Kuliga K, Xue WF. Atomic force microscopy 3D structural reconstruction of individual particles in the study of amyloid protein assemblies. Biochem Soc Trans 2024; 52:761-771. [PMID: 38600027 DOI: 10.1042/bst20230857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Recent developments in atomic force microscopy (AFM) image analysis have made three-dimensional (3D) structural reconstruction of individual particles observed on 2D AFM height images a reality. Here, we review the emerging contact point reconstruction AFM (CPR-AFM) methodology and its application in 3D reconstruction of individual helical amyloid filaments in the context of the challenges presented by the structural analysis of highly polymorphous and heterogeneous amyloid protein structures. How individual particle-level structural analysis can contribute to resolving the amyloid polymorph structure-function relationships, the environmental triggers leading to protein misfolding and aggregation into amyloid species, the influences by the conditions or minor fluctuations in the initial monomeric protein structure on the speed of amyloid fibril formation, and the extent of the different types of amyloid species that can be formed, are discussed. Future perspectives in the capabilities of AFM-based 3D structural reconstruction methodology exploiting synergies with other recent AFM technology advances are also discussed to highlight the potential of AFM as an emergent general, accessible and multimodal structural biology tool for the analysis of individual biomolecules.
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Affiliation(s)
- Claudia Chitty
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
| | - Kinga Kuliga
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
| | - Wei-Feng Xue
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
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7
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Nilsson BL, Celebi Torabfam G, Dias CL. Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations. J Phys Chem B 2024; 128:3320-3328. [PMID: 38447080 DOI: 10.1021/acs.jpcb.3c07861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Protein self-assembly plays an important role in biological systems, accounting for the formation of mesoscopic structures that can be highly symmetric as in the capsid of viruses or disordered as in molecular condensates or exhibit a one-dimensional fibrillar morphology as in amyloid fibrils. Deposits of the latter in tissues of individuals with degenerative diseases like Alzheimer's and Parkinson's has motivated extensive efforts to understand the sequence of molecular events accounting for their formation. These studies aim to identify on-pathway intermediates that may be the targets for therapeutic intervention. This detailed knowledge of fibril formation remains obscure, in part due to challenges with experimental analyses of these processes. However, important progress is being achieved for short amyloid peptides due to advances in our ability to perform completely unbiased all-atom simulations of the self-assembly process. This perspective discusses recent developments, their implications, and the hurdles that still need to be overcome to further advance the field.
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Affiliation(s)
- Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, United States
- Materials Science Program, University of Rochester, Rochester, New York 14627-0216, United States
| | - Gizem Celebi Torabfam
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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8
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Agha MM, Uversky VN. Morphological features and types of aggregated structures. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:85-109. [PMID: 38811090 DOI: 10.1016/bs.pmbts.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
In vivo, protein aggregation arises due to incorrect folding or misfolding. The aggregation of proteins into amyloid fibrils is the characteristic feature of various misfolding diseases known as amyloidosis, such as Alzheimer's and Parkinson's disease. The heterogeneous nature of these fibrils restricts the extent to which their structure may be characterized. Advancements in techniques, such as X-ray diffraction, cryo-electron microscopy, and solid-state NMR have yielded intricate insights into structures of different amyloid fibrils. These studies have unveiled a diverse range of polymorphic structures that typically conform to the cross-β amyloid pattern. This chapter provides a concise overview of the information acquired in the field of protein aggregation, with particular focus on amyloids.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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9
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Saremi S, Khajeh K. Amyloid fibril cytotoxicity and associated disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:265-290. [PMID: 38811083 DOI: 10.1016/bs.pmbts.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Misfolded proteins assemble into fibril structures that are called amyloids. Unlike usually folded proteins, misfolded fibrils are insoluble and deposit extracellularly or intracellularly. Misfolded proteins interrupt the function and structure of cells and cause amyloid disease. There is increasing evidence that the most pernicious species are oligomers. Misfolded proteins disrupt cell function and cause cytotoxicity by calcium imbalance, mitochondrial dysfunction, and intracellular reactive oxygen species. Despite profound impacts on health, social, and economic factors, amyloid diseases remain untreatable. To develop new therapeutics and to understand the pathological manifestations of amyloidosis, research into the origin and pathology of amyloidosis is urgently needed. This chapter describes the basic concept of amyloid disease and the function of atypical amyloid deposits in them.
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Affiliation(s)
- Sabereh Saremi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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10
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Miller A, Chia S, Klimont E, Knowles TPJ, Vendruscolo M, Ruggeri FS. Maturation-dependent changes in the size, structure and seeding capacity of Aβ42 amyloid fibrils. Commun Biol 2024; 7:153. [PMID: 38321144 PMCID: PMC10847148 DOI: 10.1038/s42003-024-05858-7] [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: 05/17/2023] [Accepted: 01/26/2024] [Indexed: 02/08/2024] Open
Abstract
Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile functional biomaterials. Thus, protein self-assembly has been widely studied to shed light on the properties of fibrils and their intermediates. A still open question in the field concerns the microscopic processes that underlie the long-time behaviour and properties of amyloid fibrillar assemblies. Here, we use atomic force microscopy with angstrom-sensitivity to observe that amyloid fibrils undergo a maturation process, associated with an increase in both fibril length and thickness, leading to a decrease of their density, and to a change in their cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein-based materials.
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Affiliation(s)
- Alyssa Miller
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sean Chia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ewa Klimont
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Francesco Simone Ruggeri
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen, 6703 WE, the Netherlands.
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen University, Stippeneng 4, Wageningen, 6703 WE, the Netherlands.
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11
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Samdin TD, Jones CR, Guaglianone G, Kreutzer AG, Freites JA, Wierzbicki M, Nowick JS. A β-barrel-like tetramer formed by a β-hairpin derived from Aβ. Chem Sci 2023; 15:285-297. [PMID: 38131075 PMCID: PMC10732006 DOI: 10.1039/d3sc05185d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
β-Hairpins formed by the β-amyloid peptide Aβ are building blocks of Aβ oligomers. Three different alignments of β-hairpins have been observed in the structures of Aβ oligomers or fibrils. Differences in β-hairpin alignment likely contribute to the heterogeneity of Aβ oligomers and thus impede their study at high-resolution. Here, we designed, synthesized, and studied a series of β-hairpin peptides derived from Aβ12-40 in one of these three alignments and investigated their solution-phase assembly and folding. These assays reveal the formation of tetramers and octamers that are stabilized by intermolecular hydrogen bonding interactions between Aβ residues 12-14 and 38-40 as part of an extended β-hairpin conformation. X-ray crystallographic studies of one peptide from this series reveal the formation of β-barrel-like tetramers and octamers that are stabilized by edge-to-edge hydrogen bonding and hydrophobic packing. Dye-leakage and caspase 3/7 activation assays using tetramer and octamer forming peptides from this series reveal membrane-damaging and apoptotic properties. A molecular dynamics simulation of the β-barrel-like tetramer embedded in a lipid bilayer shows membrane disruption and water permeation. The tetramers and octamers described herein provide additional models of how Aβ may assemble into oligomers and supports the hypothesis that β-hairpin alignment and topology may contribute directly to oligomer heterogeneity.
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Affiliation(s)
- Tuan D Samdin
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Chelsea R Jones
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Gretchen Guaglianone
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Adam G Kreutzer
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - J Alfredo Freites
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Michał Wierzbicki
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - James S Nowick
- Department of Chemistry, University of California Irvine California 92697-2025 USA
- Department of Pharmaceutical Sciences, University of California, Irvine Irvine California 92697-2025 USA
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12
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Levites Y, Dammer EB, Ran Y, Tsering W, Duong D, Abreha M, Gadhavi J, Lolo K, Trejo-Lopez J, Phillips JL, Iturbe A, Erqiuzi A, Moore BD, Ryu D, Natu A, Dillon KD, Torrellas J, Moran C, Ladd TB, Afroz KF, Islam T, Jagirdar J, Funk CC, Robinson M, Borchelt DR, Ertekin-Taner N, Kelly JW, Heppner FL, Johnson EC, McFarland K, Levey AL, Prokop S, Seyfried NT, Golde TE. Aβ Amyloid Scaffolds the Accumulation of Matrisome and Additional Proteins in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.568318. [PMID: 38076912 PMCID: PMC10705437 DOI: 10.1101/2023.11.29.568318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
We report a highly significant correlation in brain proteome changes between Alzheimers disease (AD) and CRND8 APP695NL/F transgenic mice. However, integrating protein changes observed in the CRND8 mice with co-expression networks derived from human AD, reveals both conserved and divergent module changes. For the most highly conserved module (M42, matrisome) we find many proteins accumulate in plaques, cerebrovascular amyloid (CAA), dystrophic processes, or a combination thereof. Overexpression of two M42 proteins, midkine (Mdk) and pleiotrophin (PTN), in CRND8 mice brains leads to increased accumulation of A β ; in plaques and in CAA; further, recombinant MDK and PTN enhance A β ; aggregation into amyloid. Multiple M42 proteins, annotated as heparan sulfate binding proteins, bind to fibrillar A β 42 and a non-human amyloid fibril in vitro. Supporting this binding data, MDK and PTN co-accumulate with transthyretin (TTR) amyloid in the heart and islet amyloid polypeptide (IAPP) amyloid in the pancreas. Our findings establish several critical insights. Proteomic changes in modules observed in human AD brains define an A β ; amyloid responsome that is well conserved from mouse model to human. Further, distinct amyloid structures may serve as scaffolds, facilitating the co-accumulation of proteins with signaling functions. We hypothesize that this co-accumulation may contribute to downstream pathological sequalae. Overall, this contextualized understanding of proteomic changes and their interplay with amyloid deposition provides valuable insights into the complexity of AD pathogenesis and potential biomarkers and therapeutic targets.
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13
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Li D, Liu C. Molecular rules governing the structural polymorphism of amyloid fibrils in neurodegenerative diseases. Structure 2023; 31:1335-1347. [PMID: 37657437 DOI: 10.1016/j.str.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/03/2023]
Abstract
Amyloid fibrils are hallmarks of various neurodegenerative diseases. The structural polymorphism of amyloid fibrils holds significant pathological importance in diseases. This review aims to provide an in-depth overview on the complexity of amyloid fibrils' structural polymorphism and its implications in disease pathogenesis. We firstly decipher the molecular rules governing the structural polymorphism of amyloid fibrils. We then discuss pivotal factors that contribute to the assortment of fibril structural polymorphs, including post-translational modifications (PTMs), disease mutations, and interacting molecules, and elucidate the structural basis of how these determinants influence amyloid fibril polymorphism. Furthermore, we underscore the need for a comprehensive understanding of the relationship between diverse fibril polymorphs and pathological activities, as well as their potential roles in therapeutic applications.
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Affiliation(s)
- Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
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14
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Stepanchuk AA, Stys PK. Amyloid dye pairs as spectral sensors for enhanced detection and differentiation of misfolded proteins. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 248:112786. [PMID: 37742497 DOI: 10.1016/j.jphotobiol.2023.112786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023]
Abstract
Protein misfolding with subsequent formation of cross-β-sheet-rich fibrils is a well-known pathological hallmark of various neurodegenerative conditions, including Alzheimer's disease (AD). Recent evidence suggests that specific protein conformations may be the primary drivers of disease progression, differentiation of which remains a challenge with conventional methods. We have previously described a unique phenomenon of light-induced fluorescence enhancement and spectral changes of the amyloid dyes K114 and BSB, and demonstrated its utility in characterizing different amyloid fibrils. In this study, we further characterize and explore the potential of photoconversion, coupled with dual-probe staining, for improved detection of heterogeneity of amyloids using silk fibers and 5xFAD mouse brain sections. BSB and K114 were paired with either Nile Red or MCAAD-3, aiming to increase the sensitivity and specificity of staining and misfolded protein detection via complementary binding and FRET. Principal component analysis of spectral data revealed significant differences between various amyloids, and was able to detect subtle amyloid pathology in the 5xFAD mouse background brain parenchyma.
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Affiliation(s)
- Anastasiia A Stepanchuk
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Cumming School of Medicine, Calgary, AB, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, University of Calgary, Cumming School of Medicine, Calgary, AB, Canada.
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15
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Turina P, Fariselli P, Capriotti E. K-Pro: Kinetics Data on Proteins and Mutants. J Mol Biol 2023; 435:168245. [PMID: 37625584 DOI: 10.1016/j.jmb.2023.168245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
The study of protein folding plays a crucial role in improving our understanding of protein function and of the relationship between genetics and phenotypes. In particular, understanding the thermodynamics and kinetics of the folding process is important for uncovering the mechanisms behind human disorders caused by protein misfolding. To address this issue, it is essential to collect and curate experimental kinetic and thermodynamic data on protein folding. K-Pro is a new database designed for collecting and storing experimental kinetic data on monomeric proteins, with a two-state folding mechanism. With 1,529 records from 62 proteins corresponding to 65 structures, K-Pro contains various kinetic parameters such as the logarithm of the folding and unfolding rates, Tanford's β and the ϕ values. When available, the database also includes thermodynamic parameters associated with the kinetic data. K-Pro features a user-friendly interface that allows browsing and downloading kinetic data of interest. The graphical interface provides a visual representation of the protein and mutants, and it is cross-linked to key databases such as PDB, UniProt, and PubMed. K-Pro is open and freely accessible through https://folding.biofold.org/k-pro and supports the latest versions of popular browsers.
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Affiliation(s)
- Paola Turina
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via F. Selmi 3, 40126 Bologna, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126 Torino, Italy
| | - Emidio Capriotti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via F. Selmi 3, 40126 Bologna, Italy.
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16
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Banavar JR, Giacometti A, Hoang TX, Maritan A, Škrbić T. A geometrical framework for thinking about proteins. Proteins 2023. [PMID: 37565735 DOI: 10.1002/prot.26567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise attraction that assembles these building blocks, while respecting their individual symmetries. Instead of seeking to mimic the complexity of proteins, we look for a simple abstraction of reality that yet captures the essence of proteins. We employ analytic calculations and detailed Monte Carlo simulations to explore some consequences of our theory. The predictions of our approach are in accord with experimental data. Our framework provides a rationalization for understanding the common characteristics of proteins. Our results show that the free energy landscape of a globular protein is pre-sculpted at the backbone level, sequences and functionalities evolve in the fixed backdrop of the folds determined by geometry and symmetry, and that protein structures are unique in being simultaneously characterized by stability, diversity, and sensitivity.
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Affiliation(s)
- Jayanth R Banavar
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon, USA
| | - Achille Giacometti
- Ca' Foscari University of Venice, Department of Molecular Sciences and Nanosystems, Venice, Italy
- European Centre for Living Technology (ECLT), Venice, Italy
| | - Trinh X Hoang
- Vietnam Academy of Science and Technology, Institute of Physics, Hanoi, Vietnam
| | - Amos Maritan
- University of Padua, Department of Physics and Astronomy, Padua, Italy
| | - Tatjana Škrbić
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon, USA
- Ca' Foscari University of Venice, Department of Molecular Sciences and Nanosystems, Venice, Italy
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17
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Zhang S, Dong H, Bian J, Li D, Liu C. Targeting amyloid proteins for clinical diagnosis of neurodegenerative diseases. FUNDAMENTAL RESEARCH 2023; 3:505-519. [PMID: 38933553 PMCID: PMC11197785 DOI: 10.1016/j.fmre.2022.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
Abnormal aggregation and accumulation of pathological amyloid proteins such as amyloid-β, Tau, and α-synuclein play key pathological roles and serve as histological hallmarks in different neurodegenerative diseases (NDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD). In addition, various post-translational modifications (PTMs) have been identified on pathological amyloid proteins and are subjected to change during disease progression. Given the central role of amyloid proteins in NDs, tremendous efforts have been made to develop amyloid-targeting strategies for clinical diagnosis and molecular classification of NDs. In this review, we summarize two major strategies for targeting amyloid aggregates, with a focus on the trials in AD diagnosis. The first strategy is a positron emission tomography (PET) scan of protein aggregation in the brain. We mainly focus on introducing the development of small-molecule PET tracers for specifically recognizing pathological amyloid fibrils. The second strategy is the detection of PTM biomarkers on amyloid proteins in cerebrospinal fluid and plasma. We discuss the pathological roles of different PTMs in diseases and how we can use the PTM profile of amyloid proteins for clinical diagnosis. Finally, we point out the potential technical challenges of these two strategies, and outline other potential strategies, as well as a combination of multiple strategies, for molecular diagnosis of NDs.
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Affiliation(s)
- Shenqing Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Bian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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18
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Avni A, Joshi A, Mukhopadhyay S. Hydrogen-Deuterium Exchange Vibrational Raman Spectroscopy Distinguishes Distinct Amyloid Polymorphs Comprising Altered Core Architecture. J Phys Chem Lett 2023:5592-5601. [PMID: 37307286 DOI: 10.1021/acs.jpclett.3c01086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibrils are ordered protein aggregates comprising a hydrogen-bonded central cross-β core displaying a structural diversity in their supramolecular packing arrangements within the core. Such an altered packing results in amyloid polymorphism that gives rise to morphological and biological strain diversities. Here, we show that vibrational Raman spectroscopy coupled with hydrogen/deuterium (H/D) exchange discerns the key structural features that are responsible for yielding diverse amyloid polymorphs. Such a noninvasive and label-free methodology allows us to structurally distinguish distinct amyloid polymorphs displaying altered hydrogen bonding and supramolecular packing within the cross-β structural motif. By using quantitative molecular fingerprinting and multivariate statistical analysis, we analyze key Raman bands for the protein backbone and side chains that allow us to capture the conformational heterogeneity and structural distributions within distinct amyloid polymorphs. Our results delineate the key molecular factors governing the structural diversity in amyloid polymorphs and can potentially simplify studying amyloid remodeling by small molecules.
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19
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Sun R, Zhang S, Liu Y, Li D. Chemical probes for investigating protein liquid-liquid phase separation and aggregation. Curr Opin Chem Biol 2023; 74:102291. [PMID: 37004350 DOI: 10.1016/j.cbpa.2023.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 04/03/2023]
Abstract
Protein liquid-liquid phase separation drives the dynamic assembly of membraneless organelles for fulfilling different physiological functions. Under diseased condition, protein may undergo liquid-to-solid condensation to form pathological amyloid aggregates closely associated with neurodegenerative diseases. Chemical probe serves as an important chemical tool not only for exploring the basic principle of the dynamic assembly of different protein condensates in vitro and in cell but also for clinical diagnosis and therapeutics of the related diseases. In this review, we first introduce chemical probes to image and regulate protein condensates. Then, we summarized three different categories of chemical probes including general amyloid dye, selective positron emission tomography tracer, and disaggregating binder, which feature distinct interaction pattern and activity upon binding to different pathological amyloid fibrillar aggregates. Next, we discuss the development of chemical probes for tracking protein amorphous aggregates in cells. Finally, we point out future direction in expanding the probes' chemical space and applications.
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Affiliation(s)
- Rui Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Shenqing Zhang
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China.
| | - Dan Li
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China; Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, World Laureates Association, Shanghai 201203, China.
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20
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Firouzi R, Sowlati-Hashjin S, Chávez-García C, Ashouri M, Karimi-Jafari MH, Karttunen M. Identification of Catechins' Binding Sites in Monomeric A β42 through Ensemble Docking and MD Simulations. Int J Mol Sci 2023; 24:ijms24098161. [PMID: 37175868 PMCID: PMC10179585 DOI: 10.3390/ijms24098161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
The assembly of the amyloid-β peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβ monomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline-in the framework of the ensemble docking strategy-to identify catechins' binding sites in monomeric Aβ42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to Aβ42. Additionally, it has been found that all the studied ligands, especially EGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of Aβ. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against Aβ.
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Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran 1496813151, Iran
| | | | - Cecilia Chávez-García
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
| | - Mitra Ashouri
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran P.O. Box 14155-6619, Iran
| | - Mohammad Hossein Karimi-Jafari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran P.O. Box 14155-6619, Iran
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 5B7, Canada
- Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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21
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Sun Y, Jack K, Ercolani T, Sangar D, Hosszu L, Collinge J, Bieschke J. Direct Observation of Competing Prion Protein Fibril Populations with Distinct Structures and Kinetics. ACS NANO 2023; 17:6575-6588. [PMID: 36802500 PMCID: PMC10100569 DOI: 10.1021/acsnano.2c12009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In prion diseases, fibrillar assemblies of misfolded prion protein (PrP) self-propagate by incorporating PrP monomers. These assemblies can evolve to adapt to changing environments and hosts, but the mechanism of prion evolution is poorly understood. We show that PrP fibrils exist as a population of competing conformers, which are selectively amplified under different conditions and can "mutate" during elongation. Prion replication therefore possesses the steps necessary for molecular evolution analogous to the quasispecies concept of genetic organisms. We monitored structure and growth of single PrP fibrils by total internal reflection and transient amyloid binding super-resolution microscopy and detected at least two main fibril populations, which emerged from seemingly homogeneous PrP seeds. All PrP fibrils elongated in a preferred direction by an intermittent "stop-and-go" mechanism, but each population possessed distinct elongation mechanisms that incorporated either unfolded or partially folded monomers. Elongation of RML and ME7 prion rods likewise exhibited distinct kinetic features. The discovery of polymorphic fibril populations growing in competition, which were previously hidden in ensemble measurements, suggests that prions and other amyloid replicating by prion-like mechanisms may represent quasispecies of structural isomorphs that can evolve to adapt to new hosts and conceivably could evade therapeutic intervention.
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Affiliation(s)
- Yuanzi Sun
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Kezia Jack
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Tiziana Ercolani
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Daljit Sangar
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Laszlo Hosszu
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - John Collinge
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Jan Bieschke
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
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22
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AlResaini S, Malik A, Alonazi M, Alhomida A, Khan JM. SDS induces amorphous, amyloid-fibril, and alpha-helical structures in the myoglobin in a concentration-dependent manner. Int J Biol Macromol 2023; 231:123237. [PMID: 36639087 DOI: 10.1016/j.ijbiomac.2023.123237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Amyloid fibrils have been linked to a number of diseases. Surfactants imitate plasma membrane lipids and induce amyloid fibrils. This study examined the effects of the anionic surfactant sodium dodecyl sulfate (SDS) at pH 4.5 on equine skeletal muscle myoglobin (E-Mb). To analyze the effect of SDS on aggregation and amyloid-fibril formation to E-Mb, we used various spectroscopic techniques (turbidity, light scattering, intrinsic fluorescence, ThT fluorescence, and circular dichroism (CD)), electrophoretic, and microscopic techniques. Turbidity, SDS-PAGE, and light scattering all indicated the formation of E-Mb aggregates at SDS concentrations ranging from 0.2 mM to 1.0 mM. In the presence of 0.4 mM SDS, far-UV CD and TEM data indicate that E-MB forms amorphous aggregates. ThT binding, Far-UV CD, and TEM findings indicate that E-Mb forms amyloid-like structures in the presence of 0.6-1.0 mM SDS. However, no aggregation was seen at SDS concentrations above 1 mM. In the presence of high SDS concentrations (> 1 mM), the E-Mb exhibited native-like α-helical structure. As a result, SDS exhibited three distinct behaviors: amorphous aggregates, amyloid-fibrils, and helix-inducer. These findings also shed light on how amyloid fibrils are formed when anionic surfactants are introduced, which is a significant takeaway.
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Affiliation(s)
- Sundus AlResaini
- Department of Biochemistry, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ajamaluddin Malik
- Department of Biochemistry, Collage of Science, King Saud University, Riyadh, Saudi Arabia.
| | - Mona Alonazi
- Department of Biochemistry, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Alhomida
- Department of Biochemistry, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Javed Masood Khan
- Department of Food and Nutrition, Facility of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
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23
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Omega-3 PUFAs as a Dietary Supplement in Senile Systemic Amyloidosis. Nutrients 2023; 15:nu15030749. [PMID: 36771455 PMCID: PMC9921273 DOI: 10.3390/nu15030749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Eicosapentaenoic acid (EPA; 20:5) and docosahexaenoic acid (DHA; 22:6), two omega-3 poly-unsaturated fatty acids (PUFAs), are the main components in oil derived from fish and other marine organisms. EPA and DHA are commercially available as dietary supplements and are considered to be very safe and contribute to guaranteeing human health. Studies report that PUFAs have a role in contrasting neurodegenerative processes related to amyloidogenic proteins, such as β-amyloid for AD, α-synuclein in PD, and transthyretin (TTR) in TTR amyloidosis. In this context, we investigated if EPA and DHA can interact directly with TTR, binding inside the thyroxin-binding pockets (T4BP) that contribute to the tetramer stabilization. The data obtained showed that EPA and DHA can contribute to stabilizing the TTR tetramer through interactions with T4BP.
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24
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Agrawal N, Skelton AA, Parisini E. A coarse-grained molecular dynamics investigation on spontaneous binding of Aβ 1-40 fibrils with cholesterol-mixed DPPC bilayers. Comput Struct Biotechnol J 2023; 21:2688-2695. [PMID: 37143763 PMCID: PMC10151222 DOI: 10.1016/j.csbj.2023.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023] Open
Abstract
Alzheimer's disease is the most common form of dementia. Its aetiology is characterized by the misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet-rich Aβ oligomers/fibrils. Although multiple experimental studies have suggested that Aβ oligomers/fibrils interact with the cell membranes and perturb their structures and dynamics, the molecular mechanism of this interaction is still not fully understood. In the present work, we have performed a total of 120 μs-long simulations to investigate the interaction between trimeric or hexameric Aβ1-40 fibrils with either a 100% DPPC bilayer, a 70% DPPC-30% cholesterol bilayer or a 50% DPPC-50% cholesterol bilayer. Our simulation data capture the spontaneous binding of the aqueous Aβ1-40 fibrils with the membranes and show that the central hydrophobic amino acid cluster, the lysine residue adjacent to it and the C-terminal hydrophobic residues are all involved in the process. Moreover, our data show that while the Aβ1-40 fibril does not bind to the 100% DPPC bilayer, its binding affinity for the membrane increases with the amount of cholesterol. Overall, our data suggest that two clusters of hydrophobic residues and one lysine help Aβ1-40 fibrils establish stable interactions with a cholesterol-rich DPPC bilayer. These residues are likely to represent potential target regions for the design of inhibitors, thus opening new avenues in structure-based drug design against Aβ oligomer/fibril-membrane interaction.
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Affiliation(s)
- Nikhil Agrawal
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia
- College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Corresponding authors at: Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia.
| | - Adam A. Skelton
- College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Emilio Parisini
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
- Corresponding authors at: Latvian Institute of Organic Synthesis, Aizkraukles 21, LV, Riga 1006, Latvia.
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25
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Nguyen PH, Derreumaux P. Insights into the Mixture of Aβ24 and Aβ42 Peptides from Atomistic Simulations. J Phys Chem B 2022; 126:10689-10696. [PMID: 36493347 DOI: 10.1021/acs.jpcb.2c07321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amyloid-β (Aβ) oligomers play a central role in Alzheimer's disease (AD). Plaques of AD patients consist of Aβ40 and Aβ42 peptides and truncated Aβ peptides. The Aβ24 peptide, identified in human AD brains, was found to impair Aβ42 clearance through the brain-blood barrier. The Aβ24 peptide was also shown to reduce Aβ42 aggregation kinetics in pure buffer, but the underlying mechanism is unknown at atomistic level. In this study, we explored the conformational ensemble of the equimolar mixture of Aβ24 and Aβ42 by replica exchange molecular dynamics simulations and compared it to our previous results on the pure Aβ42 dimer. Our simulations demonstrate that the truncation at residue 24 changes the secondary, tertiary, and quaternary structures of the dimer, offering an explanation of the slower aggregation kinetics of the mixture.
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Affiliation(s)
- Phuong H Nguyen
- Université Paris Cité, UPR 9080 CNRS, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Université Paris Cité, UPR 9080 CNRS, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, 75005 Paris, France.,Institut Universitaire de France (IUF), 75005 Paris, France
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26
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Singla D, Bhattacharya M. Salt-Induced Dissolution of Protein Aggregates. J Phys Chem B 2022; 126:8760-8770. [PMID: 36283072 DOI: 10.1021/acs.jpcb.2c06555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein aggregation is mediated by a complex interplay of noncovalent interactions and is associated with a broad range of aspects from debilitating human diseases to the food industry and therapeutic biotechnology. Deciphering the intricate roles of noncovalent interactions is of paramount importance for the design of effective inhibitory and disaggregation strategies, which remains a formidable challenge. By using a combination of spectroscopic and microscopic tools, here we show that the surfactant-mediated protein aggregation can be modulated by an intriguing interplay of hydrophobic and electrostatic effects. Additionally, our results illuminate the unique role of salt as a potent disaggregation inducer that alters the protein-surfactant electrostatic interactions and triggers the dissolution of preformed protein aggregates resulting in restoring the native protein structure. This unusual salt-induced dissolution and refolding offers a unique approach to regulating the balance between protein self-assembly and disassembly and will offer a potent strategy to design electrostatically targeted inhibitors.
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Affiliation(s)
- Deepika Singla
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
| | - Mily Bhattacharya
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
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27
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Torres-Huerta AL, Antonio-Pérez A, García-Huante Y, Alcázar-Ramírez NJ, Rueda-Silva JC. Biomolecule-Based Optical Metamaterials: Design and Applications. BIOSENSORS 2022; 12:962. [PMID: 36354471 PMCID: PMC9688573 DOI: 10.3390/bios12110962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.
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Affiliation(s)
- Ana Laura Torres-Huerta
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Aurora Antonio-Pérez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Yolanda García-Huante
- Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional (UPIITA-IPN), Mexico City 07340, Mexico
| | - Nayelhi Julieta Alcázar-Ramírez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Juan Carlos Rueda-Silva
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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28
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Baidya L, Reddy G. pH Induced Switch in the Conformational Ensemble of Intrinsically Disordered Protein Prothymosin-α and Its Implications for Amyloid Fibril Formation. J Phys Chem Lett 2022; 13:9589-9598. [PMID: 36206480 DOI: 10.1021/acs.jpclett.2c01972] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aggregation of intrinsically disordered proteins (IDPs) can lead to neurodegenerative diseases. Although there is experimental evidence that acidic pH promotes IDP monomer compaction leading to aggregation, the general mechanism is unclear. We studied the pH effect on the conformational ensemble of prothymosin-α (proTα), which is involved in multiple essential functions, and probed its role in aggregation using computer simulations. We show that compaction in the proTα dimension at low pH is due to the protein's collapse in the intermediate region (E41-D80) rich in glutamic acid residues, enhancing its β-sheet content. We observed by performing dimer simulations that the conformations with high β-sheet content could act as aggregation-prone (N*) states and nucleate the aggregation process. The simulations initiated using N* states form dimers within a microsecond time scale, whereas the non-N* states do not form dimers within this time scale. This study contributes to understanding the general principles of pH-induced IDP aggregation.
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Affiliation(s)
- Lipika Baidya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka560012, India
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29
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Trumbore CN, Raghunandan A. An Alzheimer's Disease Mechanism Based on Early Pathology, Anatomy, Vascular-Induced Flow, and Migration of Maximum Flow Stress Energy Location with Increasing Vascular Disease. J Alzheimers Dis 2022; 90:33-59. [PMID: 36155517 DOI: 10.3233/jad-220622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This paper suggests a chemical mechanism for the earliest stages of Alzheimer's disease (AD). Cerebrospinal fluid (CSF) flow stresses provide the energy needed to induce molecular conformation changes leading to AD by initiating amyloid-β (Aβ) and tau aggregation. Shear and extensional flow stresses initiate aggregation in the laboratory and in natural biophysical processes. Energy-rich CSF flow regions are mainly found in lower brain regions. MRI studies reveal flow stress "hot spots" in basal cisterns and brain ventricles that have chaotic flow properties that can distort molecules such as Aβ and tau trapped in these regions into unusual conformations. Such fluid disturbance is surrounded by tissue deformation. There is strong mapping overlap between the locations of these hot spots and of early-stage AD pathology. Our mechanism creates pure and mixed protein dimers, followed by tissue surface adsorption, and long-term tissue agitation ultimately inducing chemical reactions forming more stable, toxic oligomer seeds that initiate AD. It is proposed that different flow stress energies and flow types in different basal brain regions produce different neurotoxic aggregates. Proliferating artery hardening is responsible for enhanced heart systolic pulses that drive energetic CSF pulses, whose critical maximum systolic pulse energy location migrates further from the heart with increasing vascular disease. Two glymphatic systems, carotid and basilar, are suggested to contain the earliest Aβ and tau AD disease pathologies. A key to the proposed AD mechanism is a comparison of early chronic traumatic encephalopathy and AD pathologies. Experiments that test the proposed mechanism are needed.
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Affiliation(s)
- Conrad N Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Aditya Raghunandan
- Department of Mechanical Engineering, University of Rochester, Rochester, NY, USA
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30
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Lattice-model analysis of the effect of protein surface charge distribution on amorphous aggregation and condensation. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Donnelly KM, Coleman CM, Fuller ML, Reed VL, Smerina D, Tomlinson DS, Pearce MMP. Hunting for the cause: Evidence for prion-like mechanisms in Huntington’s disease. Front Neurosci 2022; 16:946822. [PMID: 36090278 PMCID: PMC9448931 DOI: 10.3389/fnins.2022.946822] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022] Open
Abstract
The hypothesis that pathogenic protein aggregates associated with neurodegenerative diseases spread from cell-to-cell in the brain in a manner akin to infectious prions has gained substantial momentum due to an explosion of research in the past 10–15 years. Here, we review current evidence supporting the existence of prion-like mechanisms in Huntington’s disease (HD), an autosomal dominant neurodegenerative disease caused by expansion of a CAG repeat tract in exon 1 of the huntingtin (HTT) gene. We summarize information gained from human studies and in vivo and in vitro models of HD that strongly support prion-like features of the mutant HTT (mHTT) protein, including potential involvement of molecular features of mHTT seeds, synaptic structures and connectivity, endocytic and exocytic mechanisms, tunneling nanotubes, and nonneuronal cells in mHTT propagation in the brain. We discuss mechanisms by which mHTT aggregate spreading and neurotoxicity could be causally linked and the potential benefits of targeting prion-like mechanisms in the search for new disease-modifying therapies for HD and other fatal neurodegenerative diseases.
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Affiliation(s)
- Kirby M. Donnelly
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
| | - Cevannah M. Coleman
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
| | - Madison L. Fuller
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
| | - Victoria L. Reed
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
| | - Dayna Smerina
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
| | - David S. Tomlinson
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
| | - Margaret M. Panning Pearce
- Department of Biological Sciences, University of the Sciences, Philadelphia, PA, United States
- Department of Biology, Saint Joseph’s University, Philadelphia, PA, United States
- *Correspondence: Margaret M. Panning Pearce,
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32
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Arad E, Yosefi G, Kolusheva S, Bitton R, Rapaport H, Jelinek R. Native Glucagon Amyloids Catalyze Key Metabolic Reactions. ACS NANO 2022; 16:12889-12899. [PMID: 35866668 DOI: 10.1021/acsnano.2c05166] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Glucagon is a prominent peptide hormone, playing central roles in the regulation of glucose blood-level and lipid metabolism. Formation of glucagon amyloid fibrils has been previously reported, although no biological functions of such fibrils are known. Here, we demonstrate that glucagon amyloid fibrils catalyze biologically important reactions, including esterolysis, lipid hydrolysis, and dephosphorylation. In particular, we found that glucagon fibrils catalyze dephosphorylation of adenosine triphosphate (ATP), a core metabolic reaction in cell biology. Comparative analysis of several glucagon variants allowed mapping the catalytic activity to an enzymatic pocket-like triad formed at the glucagon fibril surface, comprising the histidyl-serine domain at the N-terminus of the peptide. This study may point to previously unknown physiological roles and pathological consequences of glucagon fibrillation and supports the hypothesis that catalytic activities of native amyloid fibrils play functional roles in human physiology and disease.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Gal Yosefi
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ronit Bitton
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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33
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Brunori M, Gianni S. An Outlook on the Complexity of Protein Morphogenesis in Health and Disease. Front Mol Biosci 2022; 9:909567. [PMID: 35769915 PMCID: PMC9234464 DOI: 10.3389/fmolb.2022.909567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
The study of the mechanisms whereby proteins achieve their native functionally competent conformation has been a key issue in molecular biosciences over the last 6 decades. Nevertheless, there are several debated issues and open problems concerning some aspects of this fundamental problem. By considering the emerging complexity of the so-called “native state,” we attempt hereby to propose a personal account on some of the key topics in the field, ranging from the relationships between misfolding and diseases to the significance of protein disorder. Finally, we briefly describe the recent and exciting advances in predicting protein structures from their amino acid sequence.
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Affiliation(s)
- Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università, Rome, Italy
- Accademia Nazionale dei Lincei, Rome, Italy
- *Correspondence: Maurizio Brunori,
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università, Rome, Italy
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34
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Carroll A, Dyck PJ, de Carvalho M, Kennerson M, Reilly MM, Kiernan MC, Vucic S. Novel approaches to diagnosis and management of hereditary transthyretin amyloidosis. J Neurol Neurosurg Psychiatry 2022; 93:668-678. [PMID: 35256455 PMCID: PMC9148983 DOI: 10.1136/jnnp-2021-327909] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/12/2022] [Indexed: 12/27/2022]
Abstract
Hereditary transthyretin amyloidosis (ATTRv) is a severe, adult-onset autosomal dominant inherited systemic disease predominantly affecting the peripheral and autonomic nervous system, heart, kidney and the eyes. ATTRv is caused by mutations of the transthyretin (TTR) gene, leading to extracellular deposition of amyloid fibrils in multiple organs including the peripheral nervous system. Typically, the neuropathy associated with ATTRv is characterised by a rapidly progressive and disabling sensorimotor axonal neuropathy with early small-fibre involvement. Carpal tunnel syndrome and cardiac dysfunction frequently coexist as part of the ATTRv phenotype. Although awareness of ATTRv polyneuropathy among neurologists has increased, the rate of misdiagnosis remains high, resulting in significant diagnostic delays and accrued disability. A timely and definitive diagnosis is important, given the emergence of effective therapies which have revolutionised the management of transthyretin amyloidosis. TTR protein stabilisers diflunisal and tafamidis can delay the progression of the disease, if treated early in the course. Additionally, TTR gene silencing medications, patisiran and inotersen, have resulted in up to 80% reduction in TTR production, leading to stabilisation or slight improvement of peripheral neuropathy and cardiac dysfunction, as well as improvement in quality of life and functional outcomes. The considerable therapeutic advances have raised additional challenges, including optimisation of diagnostic techniques and management approaches in ATTRv neuropathy. This review highlights the key advances in the diagnostic techniques, current and emerging management strategies, and biomarker development for disease progression in ATTRv.
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Affiliation(s)
- Antonia Carroll
- Brain and Mind Centre, Faculty of Medicine and Health, Translational Research Collective, University of Sydney and Department of Neurology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - P James Dyck
- Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mamede de Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Department of Neurosciences and Mental Health, Hospital de Santa Maria, Lisboa, Portugal
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Molecular Medicine Laboratory Concord Repatriation General Hospital, and Concord Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
| | - Matthew C Kiernan
- Bushell Chair of Neurology, Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia.,Neurology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Steve Vucic
- Brain and Nerve Research Center, Concord Clinical School, The University of Sydney, Sydney, New South Wales, Australia
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35
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Li D, Liu C. Conformational strains of pathogenic amyloid proteins in neurodegenerative diseases. Nat Rev Neurosci 2022; 23:523-534. [DOI: 10.1038/s41583-022-00603-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2022] [Indexed: 12/11/2022]
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36
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Khurshid B, Rehman AU, Luo R, Khan A, Wadood A, Anwar J. Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations. ACS OMEGA 2022; 7:15132-15144. [PMID: 35572757 PMCID: PMC9089684 DOI: 10.1021/acsomega.2c01034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 05/14/2023]
Abstract
Glycosaminoglycans (GAGs), in particular, heparan sulfate and heparin, are found colocalized with Aβ amyloid. They have been shown to enhance fibril formation, suggesting a possible pathological connection. We have investigated heparin's assembly of the KLVFFA peptide fragment using molecular dynamics simulation, to gain a molecular-level mechanistic understanding of how GAGs enhance fibril formation. The simulations reveal an exquisite process wherein heparin accelerates peptide assembly by first "gathering" the peptide molecules and then assembling them. Heparin does not act as a mere template but is tightly coupled to the peptides, yielding a composite protofilament structure. The strong intermolecular interactions suggest composite formation to be a general feature of heparin's interaction with peptides. Heparin's chain flexibility is found to be essential to its fibril promotion activity, and the need for optimal heparin chain length and concentration has been rationalized. These insights yield design rules (flexibility; chain-length) and protocol guidance (heparin:peptide molar ratio) for developing effective heparin mimetics and other functional GAGs.
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Affiliation(s)
- Beenish Khurshid
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Ashfaq Ur Rehman
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Ray Luo
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Alamzeb Khan
- Department
of Pediatrics, Yale School of Medicine, Yale University, New Haven, Connecticut 06511, United States
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Jamshed Anwar
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, United Kingdom
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37
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Zhou Y, Hua J, Ding D, Tang Y. Interrogating amyloid aggregation with aggregation-induced emission fluorescence probes. Biomaterials 2022; 286:121605. [DOI: 10.1016/j.biomaterials.2022.121605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/26/2022]
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38
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Linking hIAPP misfolding and aggregation with type 2 diabetes mellitus: a structural perspective. Biosci Rep 2022; 42:231205. [PMID: 35475576 PMCID: PMC9118370 DOI: 10.1042/bsr20211297] [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: 02/02/2022] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
There are over 40 identified human disorders that involve certain proteins folding incorrectly, accumulating in the body causing damage to cells and organs and causing disease. Type 2 Diabetes Mellitus (T2DM) is one of these protein misfolding disorders (PMDs) and involves human islet amyloid polypeptide (hIAPP) misfolding and accumulating in parts of the body, primarily in the pancreas, causing damage to islet cells and affecting glucose regulation. In this review, we have summarised our current understanding of what causes hIAPP to misfold, what conformations are found in different parts of the body with a particular focus on what is known about the structure of hIAPP and how this links to T2DM. Understanding the molecular basis behind these misfolding events is essential for understanding the role of hIAPP to develop better therapeutics since type 2 diabetes currently affects over 4.9 million people in the United Kingdom alone and is predicted to increase as our population ages.
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39
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Takamuku M, Sugishita T, Tamaki H, Dong L, So M, Fujiwara T, Matsuki Y. Evolution of α-synuclein conformation ensemble toward amyloid fibril via liquid-liquid phase separation (LLPS) as investigated by dynamic nuclear polarization-enhanced solid-state MAS NMR. Neurochem Int 2022; 157:105345. [DOI: 10.1016/j.neuint.2022.105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
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40
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Klose D, Vemulapalli SPB, Richman M, Rudnick S, Aisha V, Abayev M, Chemerovski M, Shviro M, Zitoun D, Majer K, Wili N, Goobes G, Griesinger C, Jeschke G, Rahimipour S. Cu 2+-Induced self-assembly and amyloid formation of a cyclic D,L-α-peptide: structure and function. Phys Chem Chem Phys 2022; 24:6699-6715. [PMID: 35234757 DOI: 10.1039/d1cp05415e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a wide spectrum of neurodegenerative diseases, self-assembly of pathogenic proteins to cytotoxic intermediates is accelerated by the presence of metal ions such as Cu2+. Only low concentrations of these early transient oligomeric intermediates are present in a mixture of species during fibril formation, and hence information on the extent of structuring of these oligomers is still largely unknown. Here, we investigate dimers as the first intermediates in the Cu2+-driven aggregation of a cyclic D,L-α-peptide architecture. The unique structural and functional properties of this model system recapitulate the self-assembling properties of amyloidogenic proteins including β-sheet conformation and cross-interaction with pathogenic amyloids. We show that a histidine-rich cyclic D,L-α-octapeptide binds Cu2+ with high affinity and selectivity to generate amyloid-like cross-β-sheet structures. By taking advantage of backbone amide methylation to arrest the self-assembly at the dimeric stage, we obtain structural information and characterize the degree of local order for the dimer. We found that, while catalytic amounts of Cu2+ promote aggregation of the peptide to fibrillar structures, higher concentrations dose-dependently reduce fibrillization and lead to formation of spherical particles, showing self-assembly to different polymorphs. For the initial self-assembly step to the dimers, we found that Cu2+ is coordinated on average by two histidines, similar to self-assembled peptides, indicating that a similar binding interface is perpetuated during Cu2+-driven oligomerization. The dimer itself is found in heterogeneous conformations that undergo dynamic exchange, leading to the formation of different polymorphs at the initial stage of the aggregation process.
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Affiliation(s)
- Daniel Klose
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - Sahithya Phani Babu Vemulapalli
- NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. .,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
| | - Michal Richman
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Safra Rudnick
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel. .,Bar-Ilan Institute for Technology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Vered Aisha
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Meital Abayev
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Marina Chemerovski
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Meital Shviro
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel. .,Bar-Ilan Institute for Technology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - David Zitoun
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel. .,Bar-Ilan Institute for Technology and Advanced Materials (BINA), Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Katharina Majer
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - Nino Wili
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - Gil Goobes
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
| | - Christian Griesinger
- NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland.
| | - Shai Rahimipour
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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41
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Computational methods to predict protein aggregation. Curr Opin Struct Biol 2022; 73:102343. [PMID: 35240456 DOI: 10.1016/j.sbi.2022.102343] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 01/13/2023]
Abstract
In most cases, protein aggregation stems from the establishment of non-native intermolecular contacts. The formation of insoluble protein aggregates is associated with many human diseases and is a major bottleneck for the industrial production of protein-based therapeutics. Strikingly, fibrillar aggregates are naturally exploited for structural scaffolding or to generate molecular switches and can be artificially engineered to build up multi-functional nanomaterials. Thus, there is a high interest in rationalizing and forecasting protein aggregation. Here, we review the available computational toolbox to predict protein aggregation propensities, identify sequential or structural aggregation-prone regions, evaluate the impact of mutations on aggregation or recognize prion-like domains. We discuss the strengths and limitations of these algorithms and how they can evolve in the next future.
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Sun Y, Zhang S, Hu J, Tao Y, Xia W, Gu J, Li Y, Cao Q, Li D, Liu C. Molecular structure of an amyloid fibril formed by FUS low-complexity domain. iScience 2022; 25:103701. [PMID: 35036880 PMCID: PMC8749265 DOI: 10.1016/j.isci.2021.103701] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/22/2021] [Accepted: 12/22/2021] [Indexed: 01/25/2023] Open
Abstract
FUS is a multifunctional nuclear protein which undergoes liquid–liquid phase separation in response to stress and DNA damage. Dysregulation of FUS dynamic phase separation leads to formation of pathological fibril closely associated with neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. In this study, we determined the cryo-EM structure of a cytotoxic fibril formed by the low-complexity (LC) domain of FUS at 2.9 Å resolution. The fibril structure exhibits a new and extensive serpentine fold consisting of three motifs incorporating together via a Tyr triad. FUS LC employs 91 residues to form an enlarged and stable fibril core via hydrophilic interaction and hydrogen bonds, which is distinct from most of previously determined fibrils commonly stabilized by hydrophobic interaction. Our work reveals the structural basis underlying formation of a cytotoxic and thermostable fibril of FUS LC and sheds light on understanding the liquid-to-solid phase transition of FUS in disease. Cryo-EM structure of an amyloid fibril formed by FUS low-complexity (LC) domain FUS LC forms a novel enlarged and thermostable fibril core (FC) involving 91 residues Hydrophilic interaction and hydrogen bonds are essential in FC formation of FUS LC
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Affiliation(s)
- Yunpeng Sun
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shenqing Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jinge Gu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China.,Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
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Markulin I, Matasin M, Turk VE, Salković-Petrisic M. Challenges of repurposing tetracyclines for the treatment of Alzheimer's and Parkinson's disease. J Neural Transm (Vienna) 2022; 129:773-804. [PMID: 34982206 DOI: 10.1007/s00702-021-02457-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
The novel antibiotic-exploiting strategy in the treatment of Alzheimer's (AD) and Parkinson's (PD) disease has emerged as a potential breakthrough in the field. The research in animal AD/PD models provided evidence on the antiamyloidogenic, anti-inflammatory, antioxidant and antiapoptotic activity of tetracyclines, associated with cognitive improvement. The neuroprotective effects of minocycline and doxycycline in animals initiated investigation of their clinical efficacy in AD and PD patients which led to inconclusive results and additionally to insufficient safety data on a long-standing doxycycline and minocycline therapy in these patient populations. The safety issues should be considered in two levels; in AD/PD patients (particularly antibiotic-induced alteration of gut microbiota and its consequences), and as a world-wide threat of development of bacterial resistance to these antibiotics posed by a fact that AD and PD are widespread incurable diseases which require daily administered long-lasting antibiotic therapy. Recently proposed subantimicrobial doxycycline doses should be thoroughly explored for their effectiveness and long-term safety especially in AD/PD populations. Keeping in mind the antibacterial activity-related far-reaching undesirable effects both for the patients and globally, further work on repurposing these drugs for a long-standing therapy of AD/PD should consider the chemically modified tetracycline compounds tailored to lack antimicrobial but retain (or introduce) other activities effective against the AD/PD pathology. This strategy might reduce the risk of long-term therapy-related adverse effects (particularly gut-related ones) and development of bacterial resistance toward the tetracycline antibiotic agents but the therapeutic potential and desirable safety profile of such compounds in AD/PD patients need to be confirmed.
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Affiliation(s)
- Iva Markulin
- Community Health Centre Zagreb-Centre, Zagreb, Croatia
| | | | - Viktorija Erdeljic Turk
- Division of Clinical Pharmacology, Department of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Melita Salković-Petrisic
- Department of Pharmacology, Croatian Institute for Brain Research, University of Zagreb School of Medicine, Salata 11, 10 000, Zagreb, Croatia.
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Golde TE. Disease-Modifying Therapies for Alzheimer's Disease: More Questions than Answers. Neurotherapeutics 2022; 19:209-227. [PMID: 35229269 PMCID: PMC8885119 DOI: 10.1007/s13311-022-01201-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
Scientific advances over the last four decades have steadily infused the Alzheimer's disease (AD) field with great optimism that therapies targeting Aβ, amyloid, tau, and innate immune activation states in the brain would provide disease modification. Unfortunately, this optimistic scenario has not yet played out. Though a recent approval of the anti-Aβ aggregate binding antibody, Aduhelm (aducanumab), as a "disease-modifying therapy for AD" is viewed by some as a breakthrough, many remain unconvinced by the data underlying this approval. Collectively, we have not succeeded in changing AD from a largely untreatable, inevitable, and incurable disease to a treatable, preventable, and curable one. Here, I will review the major foci of the AD "disease-modifying" therapeutic pipeline and some of the "open questions" that remain in terms of these therapeutic approaches. I will conclude the review by discussing how we, as a field, might adjust our approach, learning from our past failures to ensure future success.
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Affiliation(s)
- Todd E Golde
- Departments of Neuroscience and Neurology, Center for Translational Research in Neurodegenerative Disease, Evelyn F. and William L. McKnight Brain Institute, Norman Fixel Institute for Neurological Diseases, University of Florida, Gainesville, FL, USA.
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Abstract
Experimental studies of amyloids encounter many challenges. There are many methods available for studying proteins, which can be applied to amyloids: from basic staining techniques, allowing visualization of fibers, to complex methods, e.g., AFM-IR used to their detailed biochemical and structural characterization in nanoscale. Which method is appropriate depends on the goal of an experiment: verification of aggregational properties of a peptide, distinguishing oligomers from mature fibers, or kinetic studies. Insolubility, rapid aggregation, and the need of using a high-purity peptide may be a limiting factor in studies involving amyloids. Moreover, the results obtained by various experimental methods often differ significantly, which may lead to misclassification of amyloid peptides. Due to ambiguity of experimental results, laborious and time-consuming analysis, bioinformatical methods become more widely used for amyloids.
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Affiliation(s)
| | - Natalia Szulc
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wrocław, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wrocław, Poland
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46
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Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022; 2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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Nasi GI, Aktypi FD, Spatharas PM, Louros NN, Tsiolaki PL, Magafa V, Trougakos IP, Iconomidou VA. Arabidopsis thaliana Plant Natriuretic Peptide Active Domain Forms Amyloid-like Fibrils in a pH-Dependent Manner. PLANTS (BASEL, SWITZERLAND) 2021; 11:9. [PMID: 35009013 PMCID: PMC8747288 DOI: 10.3390/plants11010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022]
Abstract
Plant natriuretic peptides (PNPs) are hormones that have been extracted from many different species, with the Arabidopsis thaliana PNP (AtPNP-A) being the most studied among them. AtPNP-A is a signaling molecule that consists of 130 residues and is secreted into the apoplast, under conditions of biotic or abiotic stress. AtPNP-A has distant sequence homology with human ANP, a protein that forms amyloid fibrils in vivo. In this work, we investigated the amyloidogenic properties of a 34-residue-long peptide, located within the AtPNP-A sequence, in three different pH conditions, using transmission electron microscopy, X-ray fiber diffraction, ATR FT-IR spectroscopy, Congo red and Thioflavin T staining assays. We also utilize bioinformatics tools to study its association with known plant amyloidogenic proteins and other A. thaliana proteins. Our results reveal a new case of a pH-dependent amyloid forming peptide in A. thaliana, with a potential functional role.
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Affiliation(s)
- Georgia I. Nasi
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 157 01 Athens, Greece; (G.I.N.); (F.D.A.); (P.M.S.); (N.N.L.); (P.L.T.); (I.P.T.)
| | - Foteini D. Aktypi
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 157 01 Athens, Greece; (G.I.N.); (F.D.A.); (P.M.S.); (N.N.L.); (P.L.T.); (I.P.T.)
| | - Panagiotis M. Spatharas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 157 01 Athens, Greece; (G.I.N.); (F.D.A.); (P.M.S.); (N.N.L.); (P.L.T.); (I.P.T.)
| | - Nikolaos N. Louros
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 157 01 Athens, Greece; (G.I.N.); (F.D.A.); (P.M.S.); (N.N.L.); (P.L.T.); (I.P.T.)
| | - Paraskevi L. Tsiolaki
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 157 01 Athens, Greece; (G.I.N.); (F.D.A.); (P.M.S.); (N.N.L.); (P.L.T.); (I.P.T.)
| | - Vassiliki Magafa
- Department of Pharmacy, University of Patras, 265 04 Patras, Greece;
| | - Ioannis P. Trougakos
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 157 01 Athens, Greece; (G.I.N.); (F.D.A.); (P.M.S.); (N.N.L.); (P.L.T.); (I.P.T.)
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 157 01 Athens, Greece; (G.I.N.); (F.D.A.); (P.M.S.); (N.N.L.); (P.L.T.); (I.P.T.)
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Shobo A, James N, Dai D, Röntgen A, Black C, Kwizera JR, Hancock MA, Huy Bui K, Multhaup G. The Amyloid-β 1-42-oligomer interacting peptide D-AIP possesses favorable biostability, pharmacokinetics, and brain region distribution. J Biol Chem 2021; 298:101483. [PMID: 34896396 PMCID: PMC8752909 DOI: 10.1016/j.jbc.2021.101483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 01/02/2023] Open
Abstract
We have previously developed a unique 8-amino acid Aβ42 oligomer-Interacting Peptide (AIP) as a novel anti-amyloid strategy for the treatment of Alzheimer’s disease. Our lead candidate has successfully progressed from test tubes (i.e., in vitro characterization of protease-resistant D-AIP) to transgenic flies (i.e., in vivo rescue of human Aβ42-mediated toxicity via D-AIP-supplemented food). In the present study, we examined D-AIP in terms of its stability in multiple biological matrices (i.e., ex-vivo mouse plasma, whole blood, and liver S9 fractions) using MALDI mass spectrometry, pharmacokinetics using a rapid and sensitive LC-MS method, and blood brain barrier (BBB) penetrance in WT C57LB/6 mice. D-AIP was found to be relatively stable over 3 h at 37 °C in all matrices tested. Finally, label-free MALDI imaging showed that orally administered D-AIP can readily penetrate the intact BBB in both male and female WT mice. Based upon the favorable stability, pharmacokinetics, and BBB penetration outcomes for orally administered D-AIP in WT mice, we then examined the effect of D-AIP on amyloid “seeding” in vitro (i.e., freshly monomerized versus preaggregated Aβ42). Complementary biophysical assays (ThT, TEM, and MALDI-TOF MS) showed that D-AIP can directly interact with synthetic Aβ42 aggregates to disrupt primary and/or secondary seeding events. Taken together, the unique mechanistic and desired therapeutic potential of our lead D-AIP candidate warrants further investigation, that is, testing of D-AIP efficacy on the altered amyloid/tau pathology in transgenic mouse models of Alzheimer’s disease.
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Affiliation(s)
- Adeola Shobo
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Nicholas James
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Daniel Dai
- Strathcona Anatomy Dentistry Building, McGill University, Montreal, QC, Canada
| | - Alexander Röntgen
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Corbin Black
- Strathcona Anatomy Dentistry Building, McGill University, Montreal, QC, Canada
| | - Jean-Robert Kwizera
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Mark A Hancock
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Khanh Huy Bui
- Strathcona Anatomy Dentistry Building, McGill University, Montreal, QC, Canada
| | - Gerhard Multhaup
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.
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49
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Excitation energy migration to study protein oligomerization and amyloid formation. Biophys Chem 2021; 281:106719. [PMID: 34864229 DOI: 10.1016/j.bpc.2021.106719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/22/2022]
Abstract
Excitation energy migration via homo-FRET (Förster resonance energy transfer) is a unique variant of traditional FRET that involves a non-radiative energy transfer between the dipoles of two or more chemical identical fluorophores in close proximity and with an overlap between its excitation and emission spectra. Such energy migrations between chemically identical fluorophores within the Förster distance having their dipoles oriented over a wide angular spread results in the depolarization of fluorescence anisotropy depending on the local density of the fluorophores. Therefore, this methodology can be employed to study protein oligomerization and amyloid fibril formation. The conceptual framework involves extracting structural information by identifying proximal and distal locations in supramolecular assemblies by monitoring the efficiency of homo-FRET between fluorophore-conjugated protein molecules within these supramolecular assemblies. This review highlights two such cases in which excitation energy migration via homo-FRET was used to characterize the formation of membrane-mediated β-sheet rich oligomers of the prion protein as well as to construct a site-specific 2D-proximity correlation map to probe inter-residue proximities within the highly organized amyloid fibrils of α-synuclein. Energy migration studies will find applications in studying a wide range of biomolecular assemblies such as lipid-protein complexes, oligomers, amyloids, and phase-separated condensates.
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50
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Das A. Systematic Search for a Predictor for the Clinical Observables of Alzheimer's Disease. J Phys Chem B 2021; 125:12177-12186. [PMID: 34723517 DOI: 10.1021/acs.jpcb.1c06725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
One of the prevailing life-threatening incurable neurodegenerative diseases that are presently endangering human society as a whole, and hence, baffling the entire spectrum of the scientific and pharmaceutical world, is Alzheimer's disease (AD). AD is a manifestation of self-assembly of both wild-type (sporadic) and mutated (familial) forms of the amyloid-β peptide, a proteolytic product of the amyloid precursor protein, where the self-assembly results in the genesis of pathogenic fibrillar aggregates. Currently prevailing diagnostic and hence therapeutic challenges originate from the unavailability of a specific predictor for clinical observables. The continuous emergence of novel pathogenic mutants with unpredictable phenotypes adds immensely to the nonspecific nature of the problem. The current research reports a simple physical parameter, the binding affinity of a protofilament to its protofibril, which predicts the clinical observables of familial AD with astounding accuracy and more importantly, without any adjustable parameters.
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Affiliation(s)
- Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411 008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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