1
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Todd TW, Islam NN, Cook CN, Caulfield TR, Petrucelli L. Cryo-EM structures of pathogenic fibrils and their impact on neurodegenerative disease research. Neuron 2024; 112:2269-2288. [PMID: 38834068 PMCID: PMC11257806 DOI: 10.1016/j.neuron.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 03/13/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024]
Abstract
Neurodegenerative diseases are commonly associated with the formation of aberrant protein aggregates within the brain, and ultrastructural analyses have revealed that the proteins within these inclusions often assemble into amyloid filaments. Cryoelectron microscopy (cryo-EM) has emerged as an effective method for determining the near-atomic structure of these disease-associated filamentous proteins, and the resulting structures have revolutionized the way we think about aberrant protein aggregation and propagation during disease progression. These structures have also revealed that individual fibril conformations may dictate different disease conditions, and this newfound knowledge has improved disease modeling in the lab and advanced the ongoing pursuit of clinical tools capable of distinguishing and targeting different pathogenic entities within living patients. In this review, we summarize some of the recently developed cryo-EM structures of ex vivo α-synuclein, tau, β-amyloid (Aβ), TAR DNA-binding protein 43 (TDP-43), and transmembrane protein 106B (TMEM106B) fibrils and discuss how these structures are being leveraged toward mechanistic research and therapeutic development.
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Affiliation(s)
- Tiffany W Todd
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Naeyma N Islam
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Casey N Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; Neurobiology of Disease Graduate Program, Mayo Graduate School, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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2
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Dasari AK, Sengupta U, Viverette E, Borgnia MJ, Kayed R, Lim KH. Characterization of α-synuclein oligomers formed in the presence of lipid vesicles. Biochem Biophys Rep 2024; 38:101687. [PMID: 38545462 PMCID: PMC10965497 DOI: 10.1016/j.bbrep.2024.101687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 05/23/2024] Open
Abstract
Aggregation of α-synuclein into oligomers and fibrils is associated with numerous neurodegenerative diseases such as Parkinson's disease (PD). Although the identity of the pathogenic species formed during the aggregation process is still under active debate, mounting evidence suggests that small oligomeric species rather than fibrillar aggregates are real toxic species. Isolation and characterization of small oligomers is essential to developing therapeutic strategies to prevent oligomer formation. Preparation of misfolded oligomeric species for biophysical characterization is, however, a great challenge due to their heterogenous, transient nature. Here we report the preparation of toxic and non-toxic α-synuclein oligomeric species formed at different pH values in the presence of lipid vesicles that mimic mitochondria membranes containing cardiolipin. Biophysical characterization of the lipid-induced α-synuclein oligomeric assemblies revealed that α-synuclein oligomers formed at pH 7.4 have higher surface hydrophobicity than the aggregates formed at pH 6.0. In addition, the high-pH oligomers were shown to exhibit higher toxicity than the low-pH aggregates. Structural, dynamic properties of the oligomers were also investigated by using circular dichroism (CD) and NMR spectroscopy. Our CD analyses revealed that the two oligomeric species have distinct molecular conformations, and 2D 1H/15N HSQC NMR experiments suggested that the high-pH oligomers have more extended dynamic regions than the low-pH aggregates. The distinct structural and dynamic properties of the oligomers might be associated with their different cytotoxic properties.
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Affiliation(s)
- Anvesh K.R. Dasari
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Urmi Sengupta
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Elizabeth Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Rakez Kayed
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
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3
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Han W, Wei M, Xu F, Niu Z. Aggregation and phase separation of α-synuclein in Parkinson's disease. Chem Commun (Camb) 2024; 60:6581-6590. [PMID: 38808534 DOI: 10.1039/d4cc01591f] [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: 05/30/2024]
Abstract
The deposition of α-synuclein (α-Syn) in Lewy bodies serves as a prominent pathological hallmark of Parkinson's disease (PD). Recent research has revealed that α-Syn can undergo liquid-liquid phase separation (LLPS) during its fibrillization. Over time, the maturation of the resulting condensates leads to a liquid-to-solid phase transition (LSPT) ultimately resulting in the amyloid deposition in cells which is linked to the pathogenesis and development of PD. Herein, we summarize the understanding of α-Syn aggregation which can be described by nucleation and elongation steps to obtain insights into the correlation of protein aggregation, structural polymorphism, and PD progression. Additionally, we discuss the LLPS phenomena of α-Syn and heterotypic cross-amyloid interactions with a focus on aberrant LSPT in the aggregation process. Exploring the underlying mechanisms and interplay between α-Syn aberrant aggregation, pathological phase transitions, and PD pathogenesis will shed light on potential therapeutic interventions.
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Affiliation(s)
- Wanlu Han
- School of Pharmacy, Henan University, Kaifeng, Henan 475004, China.
| | - Mengrui Wei
- School of Pharmacy, Henan University, Kaifeng, Henan 475004, China.
| | - Fei Xu
- School of Pharmacy, Henan University, Kaifeng, Henan 475004, China.
| | - Zheng Niu
- School of Pharmacy, Henan University, Kaifeng, Henan 475004, China.
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Bashir S, Aiman A, Chaudhary AA, Khan N, Ahanger IA, Sami N, Almugri EA, Ali MA, Khan SUD, Shahid M, Basir SF, Hassan MI, Islam A. Probing protein aggregation through spectroscopic insights and multimodal approaches: A comprehensive review for counteracting neurodegenerative disorders. Heliyon 2024; 10:e27949. [PMID: 38689955 PMCID: PMC11059433 DOI: 10.1016/j.heliyon.2024.e27949] [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: 12/06/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Aberrant accumulation of protein misfolding can cause aggregation and fibrillation and is one of the primary characteristic features of neurodegenerative diseases. Because they are disordered, misfolded, and aggregated proteins pose a significant setback in drug designing. The structural study of intermediate steps in these kinds of aggregated proteins will allow us to determine the conformational changes as well as the probable pathways encompassing various neurodegenerative disorders. The analysis of protein aggregates involved in neurodegenerative diseases relies on a diverse toolkit of biophysical techniques, encompassing both morphological and non-morphological methods. Additionally, Thioflavin T (ThT) assays and Circular Dichroism (CD) spectroscopy facilitate investigations into aggregation kinetics and secondary structure alterations. The collective application of these biophysical techniques empowers researchers to comprehensively unravel the intricate nature of protein aggregates associated with neurodegeneration. Furthermore, the topics covered in this review have summed up a handful of well-established techniques used for the structural analysis of protein aggregation. This multifaceted approach advances our fundamental understanding of the underlying mechanisms driving neurodegenerative diseases and informs potential therapeutic strategies.
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Affiliation(s)
- Sania Bashir
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ayesha Aiman
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Nashrah Khan
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Neha Sami
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Eman Abdullah Almugri
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Mohamed A.M. Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic Universi-ty (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, AlKharj, 11942, Saudi Arabia
| | - Seemi Farhat Basir
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
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5
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Li W, Li JY. Overlaps and divergences between tauopathies and synucleinopathies: a duet of neurodegeneration. Transl Neurodegener 2024; 13:16. [PMID: 38528629 DOI: 10.1186/s40035-024-00407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/27/2024] Open
Abstract
Proteinopathy, defined as the abnormal accumulation of proteins that eventually leads to cell death, is one of the most significant pathological features of neurodegenerative diseases. Tauopathies, represented by Alzheimer's disease (AD), and synucleinopathies, represented by Parkinson's disease (PD), show similarities in multiple aspects. AD manifests extrapyramidal symptoms while dementia is also a major sign of advanced PD. We and other researchers have sequentially shown the cross-seeding phenomenon of α-synuclein (α-syn) and tau, reinforcing pathologies between synucleinopathies and tauopathies. The highly overlapping clinical and pathological features imply shared pathogenic mechanisms between the two groups of disease. The diagnostic and therapeutic strategies seemingly appropriate for one distinct neurodegenerative disease may also apply to a broader spectrum. Therefore, a clear understanding of the overlaps and divergences between tauopathy and synucleinopathy is critical for unraveling the nature of the complicated associations among neurodegenerative diseases. In this review, we discuss the shared and diverse characteristics of tauopathies and synucleinopathies from aspects of genetic causes, clinical manifestations, pathological progression and potential common therapeutic approaches targeting the pathology, in the aim to provide a timely update for setting the scheme of disease classification and provide novel insights into the therapeutic development for neurodegenerative diseases.
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Affiliation(s)
- Wen Li
- Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, 110122, China
| | - Jia-Yi Li
- Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, 110122, China.
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund University, BMC A10, 22184, Lund, Sweden.
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6
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Zhu W, Zhang W, Chen J, Tong Y, Xu F, Pang J. Discovery of Effective Dual PROTAC Degraders for Neurodegenerative Disease-Associated Aggregates. J Med Chem 2024; 67:3448-3466. [PMID: 38356330 DOI: 10.1021/acs.jmedchem.3c01719] [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: 02/16/2024]
Abstract
The aggregation of specific proteins is a histopathological hallmark in various neurodegenerative diseases (NDs), among which Alpha-synuclein (α-Syn) and tau have received increased attention. The targeted protein degradation (TPD) strategy has been studied in the treatment of NDs, but multitarget bifunctional molecules have been ignored. Herein, a series of effective dual PROTAC degraders were developed, which could degrade α-Syn aggregates and total tau simultaneously. The degradation effects were evaluated in vitro, and the results showed that T3 could significantly knockdown α-Syn aggregates and total tau in the degradation efficiency with DC50 of 1.57 ± 0.55 and 4.09 ± 0.90 μM, respectively. Further mechanistic exploration showed that the degradation effect was mediated by the ubiquitin-proteasome system (UPS). Additionally, the therapeutic efficacy of T3 was confirmed in an MPTP-induced PD mouse model. Our results suggest that these dual PROTACs may provide a potential therapeutic strategy for NDs.
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Affiliation(s)
- Wentao Zhu
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenqian Zhang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Jian Chen
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Yichen Tong
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization & Innovative Drug Development of Chinese Ministry of Education (MOE) & Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Jiyan Pang
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
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Aubrey LD, Ninkina N, Ulamec SM, Abramycheva NY, Vasili E, Devine OM, Wilkinson M, Mackinnon E, Limorenko G, Walko M, Muwanga S, Amadio L, Peters OM, Illarioshkin SN, Outeiro TF, Ranson NA, Brockwell DJ, Buchman VL, Radford SE. Substitution of Met-38 to Ile in γ-synuclein found in two patients with amyotrophic lateral sclerosis induces aggregation into amyloid. Proc Natl Acad Sci U S A 2024; 121:e2309700120. [PMID: 38170745 PMCID: PMC10786281 DOI: 10.1073/pnas.2309700120] [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: 06/08/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
α-, β-, and γ-Synuclein are intrinsically disordered proteins implicated in physiological processes in the nervous system of vertebrates. α-synuclein (αSyn) is the amyloidogenic protein associated with Parkinson's disease and certain other neurodegenerative disorders. Intensive research has focused on the mechanisms that cause αSyn to form amyloid structures, identifying its NAC region as being necessary and sufficient for amyloid assembly. Recent work has shown that a 7-residue sequence (P1) is necessary for αSyn amyloid formation. Although γ-synuclein (γSyn) is 55% identical in sequence to αSyn and its pathological deposits are also observed in association with neurodegenerative conditions, γSyn is resilient to amyloid formation in vitro. Here, we report a rare single nucleotide polymorphism (SNP) in the SNCG gene encoding γSyn, found in two patients with amyotrophic lateral sclerosis (ALS). The SNP results in the substitution of Met38 with Ile in the P1 region of the protein. These individuals also had a second, common and nonpathological, SNP in SNCG resulting in the substitution of Glu110 with Val. In vitro studies demonstrate that the Ile38 variant accelerates amyloid fibril assembly. Contrastingly, Val110 retards fibril assembly and mitigates the effect of Ile38. Substitution of residue 38 with Leu had little effect, while Val retards, and Ala increases the rate of amyloid formation. Ile38 γSyn also results in the formation of γSyn-containing inclusions in cells. The results show how a single point substitution can enhance amyloid formation of γSyn and highlight the P1 region in driving amyloid formation in another synuclein family member.
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Affiliation(s)
- Liam D. Aubrey
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Ninkina
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sabine M. Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Natalia Y. Abramycheva
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Eftychia Vasili
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Oliver M. Devine
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Martin Wilkinson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Eilish Mackinnon
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Galina Limorenko
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Martin Walko
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Sarah Muwanga
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Leonardo Amadio
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Owen M. Peters
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
| | - Sergey N. Illarioshkin
- Laboratory of Neurobiology and Tissue Engineering, Brain Science Institute, Research Center of Neurology, Moscow125367, Russia
| | - Tiago F. Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen37075, Germany
- Max Planck Institute for Multidisciplinary Sciences, Goettingen37075, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon TyneNE2 4HH, United Kingdom
- Scientific employee with a honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen, Göttingen37075, Germany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
| | - Vladimir L. Buchman
- School of Biosciences, Cardiff University, CardiffCF10 3AX, United Kingdom
- Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod308015, Russian Federation
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, LeedsLS2 9JT, United Kingdom
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Mishra S. Emerging Trends in Cryo-EM-based Structural Studies of Neuropathological Amyloids. J Mol Biol 2023; 435:168361. [PMID: 37949311 DOI: 10.1016/j.jmb.2023.168361] [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: 09/29/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tauopathies, synucleinopathies, Aβ amyloidosis, TDP-43 proteinopathies, and prion diseases- these neurodegenerative diseases have in common the formation of amyloid filaments rich in cross-β sheets. Cryo-electron microscopy now permits the visualization of amyloid assemblies at atomic resolution, ushering a wide range of structural studies on several of these poorly understood amyloidogenic proteins. Amyloids are polymorphic with minor modulations in reaction environment affecting the overall architecture of their assembly, making amyloids an extremely challenging venture for structure-based therapeutic intervention. In 2017, the first cryo-EM structure of tau filaments from an Alzheimer's disease-affected brain established that in vitro assemblies might not necessarily reflect the native amyloid fold. Since then, brain-derived amyloid structures for several proteins across many neurodegenerative diseases have uncovered the disease-relevant amyloid folds. It has now been shown for tauopathies, synucleinopathies and TDP-43 proteinopathies, that distinct amyloid folds of the same protein might be related to different diseases. Salient features of each of these brain-derived folds are discussed in detail. It was also recently observed that seeded aggregation does not necessarily replicate the brain-derived structural fold. Owing to high throughput structure determination, some of these native amyloid folds have also been successfully replicated in vitro. In vitro replication of disease-relevant filaments will aid development of imaging ligands and defibrillating drugs. Towards this direction, recent high-resolution structures of tau filaments with positron emission tomography tracers and a defibrillating drug are also discussed. This review summarizes and celebrates the recent advancements in structural understanding of neuropathological amyloid filaments using cryo-EM.
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Affiliation(s)
- Suman Mishra
- Molecular Biophysics Unit, Biological Sciences Division, Indian Institute of Science, Bengaluru 560 012, Karnataka, India.
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9
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Zhao N, Zhang Q, Yu F, Yao X, Liu H. The α-Synuclein Monomer May Have Different Misfolding Mechanisms in the Induction of α-Synuclein Fibrils with Different Polymorphs. Biomolecules 2023; 13:biom13040682. [PMID: 37189428 DOI: 10.3390/biom13040682] [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: 02/08/2023] [Revised: 03/19/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
The aggregation of alpha-synuclein (α-Syn) is closely related to the occurrence of some neurodegenerative diseases such as Parkinson's disease. The misfolding of α-Syn monomer plays a key role in the formation of aggregates and extension of fibril. However, the misfolding mechanism of α-Syn remains elusive. Here, three different α-Syn fibrils (isolated from a diseased human brain, generated by in vitro cofactor-tau induction, and obtained by in vitro cofactor-free induction) were selected for the study. The misfolding mechanisms of α-Syn were uncovered by studying the dissociation of the boundary chains based on the conventional molecular dynamics (MD) and Steered MD simulations. The results showed that the dissociation paths of the boundary chains in the three systems were different. According to the reverse process of dissociation, we concluded that in the human brain system, the binding of the monomer and template starts from the C-terminal and gradually misfolds toward the N-terminal. In the cofactor-tau system, the monomer binding starts from residues 58-66 (contain β3), followed by the C-terminal coil (residues 67-79). Then, the N-terminal coil (residues 36-41) and residues 50-57 (contain β2) bind to the template, followed by residues 42-49 (contain β1). In the cofactor-free system, two misfolding paths were found. One is that the monomer binds to the N/C-terminal (β1/β6) and then binds to the remaining residues. The other one is that the monomer binds sequentially from the C- to N-terminal, similar to the human brain system. Furthermore, in the human brain and cofactor-tau systems, electrostatic interactions (especially from residues 58-66) are the main driving force during the misfolding process, whereas in the cofactor-free system, the contributions of electrostatic and van der Waals interactions are comparable. These results may provide a deeper understanding for the misfolding and aggregation mechanism of α-Syn.
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Affiliation(s)
- Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Zhang
- Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Faculty of Applied Sciences, Macao Polytechnic University, Macao SAR, China
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10
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Dhakal S, Robang AS, Bhatt N, Puangmalai N, Fung L, Kayed R, Paravastu AK, Rangachari V. Distinct neurotoxic TDP-43 fibril polymorphs are generated by heterotypic interactions with α-Synuclein. J Biol Chem 2022; 298:102498. [PMID: 36116552 PMCID: PMC9587012 DOI: 10.1016/j.jbc.2022.102498] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloid aggregates of specific proteins constitute important pathological hallmarks in many neurodegenerative diseases, defining neuronal degeneration and disease onset. Recently, increasing numbers of patients show comorbidities and overlaps between multiple neurodegenerative diseases, presenting distinct phenotypes. Such overlaps are often accompanied by colocalizations of more than one amyloid protein, prompting the question of whether direct interactions between different amyloid proteins could generate heterotypic amyloids. To answer this question, we investigated the effect of α-synuclein (αS) on the DNA-binding protein TDP-43 aggregation inspired by their coexistence in pathologies such as Lewy body dementia and limbic predominant age-related TDP-43 encephalopathy. We previously showed αS and prion-like C-terminal domain (PrLD) of TDP-43 synergistically interact to generate toxic heterotypic aggregates. Here, we extend these studies to investigate whether αS induces structurally and functionally distinct polymorphs of PrLD aggregates. Using αS-PrLD heterotypic aggregates generated in two different stoichiometric proportions, we show αS can affect PrLD fibril forms. PrLD fibrils show distinctive residue level signatures determined by solid state NMR, dye-binding capability, proteinase K (PK) stability, and thermal stability toward SDS denaturation. Furthremore, by gold nanoparticle labeling and transmission electron microscopy, we show the presence of both αS and PrLD proteins within the same fibrils, confirming the existence of heterotypic amyloid fibrils. We also observe αS and PrLD colocalize in the cytosol of neuroblastoma cells and show that the heterotypic PrLD fibrils selectively induce synaptic dysfunction in primary neurons. These findings establish the existence of heterotypic amyloid and provide a molecular basis for the observed overlap between synucleinopathies and TDP-43 proteinopathies.
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Affiliation(s)
- Shailendra Dhakal
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA; Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nemil Bhatt
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Nicha Puangmalai
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Leiana Fung
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, Texas, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA; Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, Mississippi, USA.
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Dasari AKR, Dillard L, Yi S, Viverette E, Hojjatian A, Sengupta U, Kayed R, Taylor KA, Borgnia MJ, Lim KH. Untwisted α-Synuclein Filaments Formed in the Presence of Lipid Vesicles. Biochemistry 2022; 61:1766-1773. [PMID: 36001818 DOI: 10.1021/acs.biochem.2c00283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accumulation of filamentous aggregates of α-synuclein is a pathological hallmark of several neurodegenerative diseases, including Parkinson's disease (PD). The interaction between α-synuclein and phospholipids has been shown to play a critical role in the aggregation of α-synuclein. Most structural studies have, however, been focused on α-synuclein filaments formed in the absence of lipids. Here, we report the structural investigation of α-synuclein filaments assembled under the quiescent condition in the presence of anionic lipid vesicles using electron microscopy (EM), including cryogenic electron microscopy (cryo-EM). Our transmission electron microscopy (TEM) analyses reveal that α-synuclein forms curly protofilaments at an early stage of aggregation. The flexible protofilaments were then converted to long filaments after a longer incubation of 30 days. More detailed structural analyses using cryo-EM reveal that the long filaments adopt untwisted structures with different diameters, which have not been observed in previous α-synuclein fibrils formed in vitro. The untwisted filaments are rather similar to straight filaments with no observable twist that are extracted from patients with dementia with Lewy bodies. Our structural studies highlight the conformational diversity of α-synuclein filaments, requiring additional structural investigation of not only more ex vivo α-synuclein filaments but also in vitro α-synuclein filaments formed in the presence of diverse cofactors to better understand the molecular basis of diverse molecular conformations of α-synuclein filaments.
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Affiliation(s)
- Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Lucas Dillard
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Sujung Yi
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
| | - Elizabeth Viverette
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Alimohammad Hojjatian
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4380, United States
| | - Urmi Sengupta
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Rakez Kayed
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Kenneth A Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4380, United States
| | - Mario Juan Borgnia
- Department of Health and Human Services, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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Pan L, Li C, Meng L, Tian Y, He M, Yuan X, Zhang G, Zhang Z, Xiong J, Chen G, Zhang Z. Tau accelerates α-synuclein aggregation and spreading in Parkinson's disease. Brain 2022; 145:3454-3471. [PMID: 35552614 DOI: 10.1093/brain/awac171] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/15/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
The aggregation and prion-like propagation of α-synuclein are involved in the pathogenesis of Parkinson's disease. However, the underlying mechanisms regulating the assembly and spreading of α-synuclein fibrils remain poorly understood. Tau co-deposits with α-synuclein in the brains of Parkinson's disease patients, suggesting a pathological interplay between them. Here we show that tau interacts with α-synuclein and accelerates its aggregation. Compared with pure α-synuclein fibrils, the tau-modified α-synuclein fibrils show enhanced seeding activity, inducing mitochondrial dysfunction, synaptic impairment, and neurotoxicity in vitro. Injection of the tau-modified α-synuclein fibrils into the striatum of mice induces more severe α-synuclein pathology, motor dysfunction, and cognitive impairment when compared with the mice injected with pure α-synuclein fibrils. Knockout of tau attenuates the propagation of α-synuclein pathology and Parkinson's disease-like symptoms both in mice injected with α-syn fibrils and α-syn A53 T transgenic mice. In conclusion, tau facilitates α-synuclein aggregation and propagation in Parkinson's disease.
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Affiliation(s)
- Lina Pan
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Chunrui Li
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lanxia Meng
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ye Tian
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Mingyang He
- Hubei Provincial Institute for Food Supervision and Test, Wuhan 430070, China
| | - Xin Yuan
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Guoxin Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhaohui Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jing Xiong
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Guiqin Chen
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhentao Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
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13
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Sengupta U, Kayed R. Amyloid β, Tau, and α-Synuclein aggregates in the pathogenesis, prognosis, and therapeutics for neurodegenerative diseases. Prog Neurobiol 2022; 214:102270. [DOI: 10.1016/j.pneurobio.2022.102270] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 12/11/2022]
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14
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Kitoka K, Skrabana R, Gasparik N, Hritz J, Jaudzems K. NMR Studies of Tau Protein in Tauopathies. Front Mol Biosci 2021; 8:761227. [PMID: 34859051 PMCID: PMC8632555 DOI: 10.3389/fmolb.2021.761227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Tauopathies, including Alzheimer's disease (AD), are the most troublesome of all age-related chronic conditions, as there are no well-established disease-modifying therapies for their prevention and treatment. Spatio-temporal distribution of tau protein pathology correlates with cognitive decline and severity of the disease, therefore, tau protein has become an appealing target for therapy. Current knowledge of the pathological effects and significance of specific species in the tau aggregation pathway is incomplete although more and more structural and mechanistic insights are being gained using biophysical techniques. Here, we review the application of NMR to structural studies of various tau forms that appear in its aggregation process, focusing on results obtained from solid-state NMR. Furthermore, we discuss implications from these studies and their prospective contribution to the development of new tauopathy therapies.
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Affiliation(s)
- Kristine Kitoka
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Rostislav Skrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- AXON Neuroscience R&D Services SE, Bratislava, Slovakia
| | - Norbert Gasparik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristaps Jaudzems
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
- Faculty of Chemistry, University of Latvia, Riga, Latvia
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