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Rahman MU, Bano S, Hong X, Gu RX, Chen HF. Early Aggregation Mechanism of SOD1 28-38 Based on Force Field Parameter of 5-Cyano-Tryptophan. J Chem Inf Model 2024; 64:3942-3952. [PMID: 38652017 DOI: 10.1021/acs.jcim.4c00289] [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: 04/25/2024]
Abstract
The aggregation of superoxide dismutase 1 (SOD1) results in amyloid deposition and is involved in familial amyotrophic lateral sclerosis, a fatal motor neuron disease. There have been extensive studies of its aggregation mechanism. Noncanonical amino acid 5-cyano-tryptophan (5-CN-Trp), which has been incorporated into the amyloid segments of SOD1 as infrared probes to increase the structural sensitivity of IR spectroscopy, is found to accelerate the overall aggregation rate and potentially modulate the aggregation process. Despite these observations, the underlying mechanism remains elusive. Here, we optimized the force field parameters of 5-CN-Trp and then used molecular dynamics simulation along with the Markov state model on the SOD128-38 dimer to explore the kinetics of key intermediates in the presence and absence of 5-CN-Trp. Our findings indicate a significantly increased probability of protein aggregate formation in 5CN-Trp-modified ensembles compared to wildtype. Dimeric β-sheets of different natures were observed exclusively in the 5CN-Trp-modified peptides, contrasting with wildtype simulations. Free-energy calculations and detailed analyses of the dimer structure revealed augmented interstrand interactions attributed to 5-CN-Trp, which contributed more to peptide affinity than any other residues. These results explored the key events critical for the early nucleation of amyloid-prone proteins and also shed light on the practice of using noncanonical derivatives to study the aggregation mechanism.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, Department of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Saira Bano
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, Department of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaokun Hong
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, Department of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruo-Xu Gu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, Department of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, Department of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Pradhan AK, Neumüller T, Klug C, Fuchs S, Schlegel M, Ballmann M, Tartler KJ, Pianos A, Garcia MS, Liere P, Schumacher M, Kreuzer M, Rupprecht R, Rammes G. Chronic administration of XBD173 ameliorates cognitive deficits and neuropathology via 18 kDa translocator protein (TSPO) in a mouse model of Alzheimer's disease. Transl Psychiatry 2023; 13:332. [PMID: 37891168 PMCID: PMC10611770 DOI: 10.1038/s41398-023-02630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Alzheimer's disease (AD) is characterized by the accumulation of β-amyloid peptide (Aβ). It affects cognition and leads to memory impairment. The mitochondrial translocator protein (TSPO) plays an essential role in maintaining mitochondrial homeostasis and has been implicated in several neuronal disorders or neuronal injuries. Ligands targeting the mitochondrial translocator protein (18 kDa), promote neurosteroidogenesis and may be neuroprotective. To study whether the TSPO ligand XBD173 may exert early neuroprotective effects in AD pathology we investigated the impact of XBD173 on amyloid toxicity and neuroplasticity in mouse models of AD. We show that XBD173 (emapunil), via neurosteroid-mediated signaling and delta subunit-containing GABAA receptors, prevents the neurotoxic effect of Aβ on long-term potentiation (CA1-LTP) in the hippocampus and prevents the loss of spines. Chronic but not acute administration of XBD173 ameliorates spatial learning deficits in transgenic AD mice with arctic mutation (ArcAβ). The heterozygous TSPO-knockout crossed with the transgenic arctic mutation model of AD mice (het TSPOKO X ArcAβ) treated with XBD173 does not show this improvement in spatial learning suggesting TSPO is needed for procognitive effects of XBD173. The neuroprotective profile of XBD173 in AD pathology is further supported by a reduction in plaques and soluble Aβ levels in the cortex, increased synthesis of neurosteroids, rescued spine density, reduction of complement protein C1q deposits, and reduced astrocytic phagocytosis of functional synapses both in the hippocampus and cortex. Our findings suggest that XBD173 may exert therapeutic effects via TSPO in a mouse model of AD.
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Affiliation(s)
- Arpit Kumar Pradhan
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany.
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-Universität München, Martinsried, Germany.
| | - Tatjana Neumüller
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
| | - Claudia Klug
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
| | - Severin Fuchs
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
| | - Martin Schlegel
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
| | - Markus Ballmann
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
| | - Katharina Johanna Tartler
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
| | - Antoine Pianos
- U1195 Inserm and University Paris-Saclay, 80 rue du Général Leclerc, Le Kremlin-Bicêtre, 94276, France
| | - Maria Sanchez Garcia
- U1195 Inserm and University Paris-Saclay, 80 rue du Général Leclerc, Le Kremlin-Bicêtre, 94276, France
| | - Philippe Liere
- U1195 Inserm and University Paris-Saclay, 80 rue du Général Leclerc, Le Kremlin-Bicêtre, 94276, France
| | - Michael Schumacher
- U1195 Inserm and University Paris-Saclay, 80 rue du Général Leclerc, Le Kremlin-Bicêtre, 94276, France
| | - Matthias Kreuzer
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
| | - Rainer Rupprecht
- Department of Psychiatry and Psychotherapy, University Regensburg, Regensburg, Germany
| | - Gerhard Rammes
- Klinik für Anaesthesiologie und Intensivmedizin der Technischen Universität München, Klinikum rechts der Isar, Munich, Germany
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Kulichikhin KY, Malikova OA, Zobnina AE, Zalutskaya NM, Rubel AA. Interaction of Proteins Involved in Neuronal Proteinopathies. Life (Basel) 2023; 13:1954. [PMID: 37895336 PMCID: PMC10608209 DOI: 10.3390/life13101954] [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: 08/15/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Proteinopathy is characterized by the accumulation of aggregates of a specific protein in a target organ, tissue, or cell. The aggregation of the same protein can cause different pathologies as single protein can adopt various amyloidogenic, disease-specific conformations. The conformation governs the interaction of amyloid aggregates with other proteins that are prone to misfolding and, thus, determines disease-specific spectrum of concomitant pathologies. In this regard, a detailed description of amyloid protein conformation as well as spectrum of its interaction with other proteins become a key point for drafting of precise description of the disease. The majority of clinical cases of neuronal proteinopathies is caused by the aggregation of rather limited range of amyloidogenic proteins. Here, we provided the characterization of pathologies, related to the aggregation of amyloid β peptide, tau protein, α-synuclein, TDP-43, and amylin, giving a short description of pathologies themselves, recent advances in elucidation of misfolded protein conformation, with emphasis on those protein aggregates extracted from biological samples, what is known about the interaction of this proteins, and the influence of this interaction on the progression of underlying disease and comorbidities.
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Affiliation(s)
- Konstantin Y. Kulichikhin
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
| | - Oksana A. Malikova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
| | - Anastasia E. Zobnina
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
| | - Natalia M. Zalutskaya
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, 192019 St. Petersburg, Russia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (O.A.M.); (A.E.Z.)
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4
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Scheres SHW, Ryskeldi-Falcon B, Goedert M. Molecular pathology of neurodegenerative diseases by cryo-EM of amyloids. Nature 2023; 621:701-710. [PMID: 37758888 DOI: 10.1038/s41586-023-06437-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 07/14/2023] [Indexed: 09/29/2023]
Abstract
Abnormal assembly of tau, α-synuclein, TDP-43 and amyloid-β proteins into amyloid filaments defines most human neurodegenerative diseases. Genetics provides a direct link between filament formation and the causes of disease. Developments in cryo-electron microscopy (cryo-EM) have made it possible to determine the atomic structures of amyloids from postmortem human brains. Here we review the structures of brain-derived amyloid filaments that have been determined so far and discuss their impact on research into neurodegeneration. Whereas a given protein can adopt many different filament structures, specific amyloid folds define distinct diseases. Amyloid structures thus provide a description of neuropathology at the atomic level and a basis for studying disease. Future research should focus on model systems that replicate the structures observed in disease to better understand the molecular mechanisms of disease and develop improved diagnostics and therapies.
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Affiliation(s)
- Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | | | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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5
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Zhang W, Liu M, Wang Y, Wang X, Wang R, Li S, Yu L, Zhang F, Wang C. β-Sheet Assembly Translates Conservative Single-Site Mutation into a Perturbation in Macroscopic Structure. NANO LETTERS 2023; 23:2370-2378. [PMID: 36897606 DOI: 10.1021/acs.nanolett.3c00311] [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: 06/18/2023]
Abstract
Transferring structural information from amino acid sequence to macroscale assembly is a challenging approach for designing protein quaternary structure. However, the pathway by which the slight variations in sequence result in a global perturbation effect on the assembled structure is unknown. Herein, we design two synthetic peptides, QNL-His and QNL-Arg, with one amino acid substitution and use scanning tunneling microscopy (STM) to image individual peptides in the assembled state. The submolecular resolution of STM enables us to determine the folding structure and β-sheet supramolecular organization of peptides. QNL-His and QNL-Arg differ in their β-strand length distribution in pleated β-sheet association. These structural variations lead to distinguishable outcomes in their β-sheet assembled fibrils and phase transitions. The comparison of QNL-His versus QNL-Arg structures and macroscopic properties unveils the role of assembly to amplify the structural variations associated with a single-site mutation from a single-molecule scale to a macroscopic scale.
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Affiliation(s)
- Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Mingwei Liu
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Yang Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Xin Wang
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Ruonan Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Shuyuan Li
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
| | - Feiyi Zhang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, Jiangsu 212013, P. R. China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Haihe Laboratory of Cell Ecosystem, Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, P. R. China
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6
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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7
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Hu J, Zhao Y, Li Y. Rationally designed amyloid inhibitors based on amyloid-related structural studies. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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8
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Behl T, Kaur D, Sehgal A, Singh S, Makeen HA, Albratty M, Abdellatif AAH, Dachani SR, Bungau S. Exploring the potential role of rab5 protein in endo-lysosomal impairment in Alzheimer's disease. Biomed Pharmacother 2022; 148:112773. [PMID: 35245734 DOI: 10.1016/j.biopha.2022.112773] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/27/2022] [Indexed: 11/02/2022] Open
Abstract
Growing evidence suggests that neuronal dysfunction in the endo-lysosomal and autophagic processes contributes to the onset and progression of neurodegenerative diseases such as Alzheimer's disease (AD). Since they are the primary cellular systems involved in the production and clearance of aggregated amyloid plaques, endo-lysosomal or autophagic equilibrium must be maintained throughout life. As a result, variations in the autophagic and endo-lysosomal torrent, as a measure of degenerative function in these sections or pathways, may have a direct impact on disease-related processes, such as Aß clearance from the brain and interneuronal deposition of Aß and tau aggregates, thus disrupting synaptic plasticity. The discovery of several chromosomal factors for Alzheimer's disease that are clinically linked to regulation of the endocytic pathway, including protein aggregation and removal, supports the theory that the endo-lysosomal/autophagic torrent is more susceptible to impairment, especially as people age, thus catalysing the onset of disease. Although the role of endo-lysosomal/autophagic dysfunction in neurodegeneration has progressed in recent years, the field remains underdeveloped. Because of its possible therapeutic implications in Alzheimer's disease, further study is needed to explain the possibilities for effective autophagy regulation.
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Affiliation(s)
- Tapan Behl
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India.
| | - Dapinder Kaur
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Aayush Sehgal
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Sukhbir Singh
- Department of Pharmacology, Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Hafiz A Makeen
- Pharmacy Practice Research Unit, Clinical Pharmacy, Department, College of Pharmacy, Jazan University, P.O. Box-114, Jazan 45142, Saudi Arabia
| | - Mohammed Albratty
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
| | - Ahmed A H Abdellatif
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia; Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Sudharshan Reddy Dachani
- Department of Pharmacy Practice & Pharmacology, College of Pharmacy, Shaqra University, Al-Dawadmi Campus, Al-Dawadmi 11961, Saudi Arabia
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410073 Oradea, Romania.
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9
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Abstract
In this highlight, we describe the construction of supramolecular single/double/triple-helical assemblies from small di/tri/tetrapeptides and their applications.
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Affiliation(s)
- Rajat Subhra Giri
- Department of Chemistry, Laboratory of Peptide and Amyloid Research, Indian Institute of Technology Guwahati, Assam-781039, India
| | - Bhubaneswar Mandal
- Department of Chemistry, Laboratory of Peptide and Amyloid Research, Indian Institute of Technology Guwahati, Assam-781039, India
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10
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Zhang Q, Wang B, Zhang Y, Yang J, Deng B, Ding B, Zhong D. Probing Intermolecular Interactions of Amyloidogenic Fragments of SOD1 by Site-Specific Tryptophan and Its Noncanonical Derivative. J Phys Chem B 2021; 125:13088-13098. [PMID: 34812635 DOI: 10.1021/acs.jpcb.1c07175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transient amyloid intermediates are likely to be cytotoxic and play an essential role in amyloid-associated neurodegenerative diseases. Characterization of their structural and dynamic evolution is the key to elucidating the molecular mechanism of amyloid formation. Here, combining circular dichroism (CD), exciton couplet theory, and Fourier transform infrared spectroscopy with site-specific tryptophan (Trp) and its noncanonical derivative 5-cyano-tryptochan (Trp5CN), we developed a method to monitor strand-to-strand tertiary and sheet-to-sheet quaternary interactions in the aggregation cascades of an amyloidogenic fragment from protein SOD128-38 (with the sequence KVKVWGSIKGL). We found that the exciton couplet generated from the Bb band of Trp can be used as a probe for side chain interactions. Its sensitivity can be further improved by four times with the incorporation of Trp5CN. We further observed a red-shift of ∼2 cm-1 and a broadening of ∼2 cm-1 in the IR band generated from the CN stretch during the aggregation, which we attributed to the transition from a corkscrew-like structure to a cross-linked intermediate phase. We show here that the integration of optical methods with unique aromatic side chain-related probes is able to elucidate amyloid intermolecular interactions and even capture elusive transient intermediates on and off the amyloid assembling pathway.
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Affiliation(s)
- Qin Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bingyao Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifei Zhang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Yang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bodan Deng
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.,Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Raskatov JA, Foley A, Louis JM, Yau WM, Tycko R. Constraints on the Structure of Fibrils Formed by a Racemic Mixture of Amyloid-β Peptides from Solid-State NMR, Electron Microscopy, and Theory. J Am Chem Soc 2021; 143:13299-13313. [PMID: 34375097 PMCID: PMC8456612 DOI: 10.1021/jacs.1c06339] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Previous studies have shown that racemic mixtures of 40- and 42-residue amyloid-β peptides (d,l-Aβ40 and d,l-Aβ42) form amyloid fibrils with accelerated kinetics and enhanced stability relative to their homochiral counterparts (l-Aβ40 and l-Aβ42), suggesting a "chiral inactivation" approach to abrogating the neurotoxicity of Aβ oligomers (Aβ-CI). Here we report a structural study of d,l-Aβ40 fibrils, using electron microscopy, solid-state nuclear magnetic resonance (NMR), and density functional theory (DFT) calculations. Two- and three-dimensional solid-state NMR spectra indicate molecular conformations in d,l-Aβ40 fibrils that resemble those in known l-Aβ40 fibril structures. However, quantitative measurements of 13C-13C and 15N-13C distances in selectively labeled d,l-Aβ40 fibril samples indicate a qualitatively different supramolecular structure. While cross-β structures in mature l-Aβ40 fibrils are comprised of in-register, parallel β-sheets, our data indicate antiparallel β-sheets in d,l-Aβ40 fibrils, with alternation of d and l molecules along the fibril growth direction, i.e., antiparallel "rippled sheet" structures. The solid-state NMR data suggest the coexistence of d,l-Aβ40 fibril polymorphs with three different registries of intermolecular hydrogen bonds within the antiparallel rippled sheets. DFT calculations support an energetic preference for antiparallel alignments of the β-strand segments identified by solid-state NMR. These results provide insight into the structural basis for Aβ-CI and establish the importance of rippled sheets in self-assembly of full-length, naturally occurring amyloidogenic peptides.
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Affiliation(s)
- Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - Alejandro Foley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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12
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Ma YW, Lin TY, Tsai MY. Fibril Surface-Dependent Amyloid Precursors Revealed by Coarse-Grained Molecular Dynamics Simulation. Front Mol Biosci 2021; 8:719320. [PMID: 34422910 PMCID: PMC8378332 DOI: 10.3389/fmolb.2021.719320] [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: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 01/05/2023] Open
Abstract
Amyloid peptides are known to self-assemble into larger aggregates that are linked to the pathogenesis of many neurodegenerative disorders. In contrast to primary nucleation, recent experimental and theoretical studies have shown that many toxic oligomeric species are generated through secondary processes on a pre-existing fibrillar surface. Nucleation, for example, can also occur along the surface of a pre-existing fibril—secondary nucleation—as opposed to the primary one. However, explicit pathways are still not clear. In this study, we use molecular dynamics simulation to explore the free energy landscape of a free Abeta monomer binding to an existing fibrillar surface. We specifically look into several potential Abeta structural precursors that might precede some secondary events, including elongation and secondary nucleation. We find that the overall process of surface-dependent events can be described at least by the following three stages: 1. Free diffusion 2. Downhill guiding 3. Dock and lock. And we show that the outcome of adding a new monomer onto a pre-existing fibril is pathway-dependent, which leads to different secondary processes. To understand structural details, we have identified several monomeric amyloid precursors over the fibrillar surfaces and characterize their heterogeneity using a probability contact map analysis. Using the frustration analysis (a bioinformatics tool), we show that surface heterogeneity correlates with the energy frustration of specific local residues that form binding sites on the fibrillar structure. We further investigate the helical twisting of protofilaments of different sizes and observe a length dependence on the filament twisting. This work presents a comprehensive survey over the properties of fibril growth using a combination of several openMM-based platforms, including the GPU-enabled openAWSEM package for coarse-grained modeling, MDTraj for trajectory analysis, and pyEMMA for free energy calculation. This combined approach makes long-timescale simulation for aggregation systems as well as all-in-one analysis feasible. We show that this protocol allows us to explore fibril stability, surface binding affinity/heterogeneity, as well as fibrillar twisting. All these properties are important for understanding the molecular mechanism of surface-catalyzed secondary processes of fibril growth.
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Affiliation(s)
- Yuan-Wei Ma
- Department of Chemistry, Tamkang University, New Taipei City, Taiwan
| | - Tong-You Lin
- Department of Chemistry, Tamkang University, New Taipei City, Taiwan
| | - Min-Yeh Tsai
- Department of Chemistry, Tamkang University, New Taipei City, Taiwan
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13
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Rizvi A, Mulvey JT, Carpenter BP, Talosig R, Patterson JP. A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope. Chem Rev 2021; 121:14232-14280. [PMID: 34329552 DOI: 10.1021/acs.chemrev.1c00189] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.
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Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Justin T Mulvey
- Department of Materials Science and Engineering, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Brooke P Carpenter
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Rain Talosig
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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14
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Lutter L, Aubrey LD, Xue WF. On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies. J Mol Biol 2021; 433:167124. [PMID: 34224749 DOI: 10.1016/j.jmb.2021.167124] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/20/2021] [Accepted: 06/26/2021] [Indexed: 12/24/2022]
Abstract
The prediction of highly ordered three-dimensional structures of amyloid protein fibrils from the amino acid sequences of their monomeric self-assembly precursors constitutes a challenging and unresolved aspect of the classical protein folding problem. Because of the polymorphic nature of amyloid assembly whereby polypeptide chains of identical amino acid sequences under identical conditions are capable of self-assembly into a spectrum of different fibril structures, the prediction of amyloid structures from an amino acid sequence requires a detailed and holistic understanding of its assembly free energy landscape. The full extent of the structure space accessible to the cross-β molecular architecture of amyloid must also be resolved. Here, we review the current understanding of the diversity and the individuality of amyloid structures, and how the polymorphic landscape of amyloid links to biology and disease phenotypes. We present a comprehensive review of structural models of amyloid fibrils derived by cryo-EM, ssNMR and AFM to date, and discuss the challenges ahead for resolving the structural basis and the biological consequences of polymorphic amyloid assemblies.
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Affiliation(s)
- Liisa Lutter
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Liam D Aubrey
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Wei-Feng Xue
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK.
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15
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Lau HHC, Ingelsson M, Watts JC. The existence of Aβ strains and their potential for driving phenotypic heterogeneity in Alzheimer's disease. Acta Neuropathol 2021; 142:17-39. [PMID: 32743745 DOI: 10.1007/s00401-020-02201-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/17/2022]
Abstract
Reminiscent of the human prion diseases, there is considerable clinical and pathological variability in Alzheimer's disease, the most common human neurodegenerative condition. As in prion disorders, protein misfolding and aggregation is a hallmark feature of Alzheimer's disease, where the initiating event is thought to be the self-assembly of Aβ peptide into aggregates that deposit in the central nervous system. Emerging evidence suggests that Aβ, similar to the prion protein, can polymerize into a conformationally diverse spectrum of aggregate strains both in vitro and within the brain. Moreover, certain types of Aβ aggregates exhibit key hallmarks of prion strains including divergent biochemical attributes and the ability to induce distinct pathological phenotypes when intracerebrally injected into mouse models. In this review, we discuss the evidence demonstrating that Aβ can assemble into distinct strains of aggregates and how such strains may be primary drivers of the phenotypic heterogeneity in Alzheimer's disease.
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16
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Wang K, Na L, Duan M. The Pathogenesis Mechanism, Structure Properties, Potential Drugs and Therapeutic Nanoparticles against the Small Oligomers of Amyloid-β. Curr Top Med Chem 2021; 21:151-167. [PMID: 32938351 DOI: 10.2174/1568026620666200916123000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/02/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022]
Abstract
Alzheimer's Disease (AD) is a devastating neurodegenerative disease that affects millions of people in the world. The abnormal aggregation of amyloid β protein (Aβ) is regarded as the key event in AD onset. Meanwhile, the Aβ oligomers are believed to be the most toxic species of Aβ. Recent studies show that the Aβ dimers, which are the smallest form of Aβ oligomers, also have the neurotoxicity in the absence of other oligomers in physiological conditions. In this review, we focus on the pathogenesis, structure and potential therapeutic molecules against small Aβ oligomers, as well as the nanoparticles (NPs) in the treatment of AD. In this review, we firstly focus on the pathogenic mechanism of Aβ oligomers, especially the Aβ dimers. The toxicity of Aβ dimer or oligomers, which attributes to the interactions with various receptors and the disruption of membrane or intracellular environments, were introduced. Then the structure properties of Aβ dimers and oligomers are summarized. Although some structural information such as the secondary structure content is characterized by experimental technologies, detailed structures are still absent. Following that, the small molecules targeting Aβ dimers or oligomers are collected; nevertheless, all of these ligands have failed to come into the market due to the rising controversy of the Aβ-related "amyloid cascade hypothesis". At last, the recent progress about the nanoparticles as the potential drugs or the drug delivery for the Aβ oligomers are present.
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Affiliation(s)
- Ke Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liu Na
- School of Biological and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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17
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Creekmore BC, Chang YW, Lee EB. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Aggregates. J Neuropathol Exp Neurol 2021; 80:514-529. [PMID: 33970243 PMCID: PMC8177849 DOI: 10.1093/jnen/nlab039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Neurogenerative diseases are characterized by diverse protein aggregates with a variety of microscopic morphologic features. Although ultrastructural studies of human neurodegenerative disease tissues have been conducted since the 1960s, only recently have near-atomic resolution structures of neurodegenerative disease aggregates been described. Solid-state nuclear magnetic resonance spectroscopy and X-ray crystallography have provided near-atomic resolution information about in vitro aggregates but pose logistical challenges to resolving the structure of aggregates derived from human tissues. Recent advances in cryo-electron microscopy (cryo-EM) have provided the means for near-atomic resolution structures of tau, amyloid-β (Aβ), α-synuclein (α-syn), and transactive response element DNA-binding protein of 43 kDa (TDP-43) aggregates from a variety of diseases. Importantly, in vitro aggregate structures do not recapitulate ex vivo aggregate structures. Ex vivo tau aggregate structures indicate individual tauopathies have a consistent aggregate structure unique from other tauopathies. α-syn structures show that even within a disease, aggregate heterogeneity may correlate to disease course. Ex vivo structures have also provided insight into how posttranslational modifications may relate to aggregate structure. Though there is less cryo-EM data for human tissue-derived TDP-43 and Aβ, initial structural studies provide a basis for future endeavors. This review highlights structural variations across neurodegenerative diseases and reveals fundamental differences between experimental systems and human tissue derived protein inclusions.
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Affiliation(s)
- Benjamin C Creekmore
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yi-Wei Chang
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Send correspondence to: Edward B. Lee, MD, PhD, Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 613A Stellar Chance Laboratories, 422 Curie Blvd., Philadelphia, PA 19104, USA; E-mail:
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18
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Dolai G, Giri RS, Roy S, Mandal B. Crystal structure and supramolecular arrangement of heterochiral tripeptides. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Gobinda Dolai
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
| | - Rajat Subhra Giri
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
| | - Sayanta Roy
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
| | - Bhubaneswar Mandal
- Department of Chemistry, Laboratory of Peptide and Amyloid Research Indian Institute of Technology Guwahati Assam India
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19
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 385] [Impact Index Per Article: 128.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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20
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Gracia P, Camino JD, Volpicelli-Daley L, Cremades N. Multiplicity of α-Synuclein Aggregated Species and Their Possible Roles in Disease. Int J Mol Sci 2020; 21:E8043. [PMID: 33126694 PMCID: PMC7663424 DOI: 10.3390/ijms21218043] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
α-Synuclein amyloid aggregation is a defining molecular feature of Parkinson's disease, Lewy body dementia, and multiple system atrophy, but can also be found in other neurodegenerative disorders such as Alzheimer's disease. The process of α-synuclein aggregation can be initiated through alternative nucleation mechanisms and dominated by different secondary processes giving rise to multiple amyloid polymorphs and intermediate species. Some aggregated species have more inherent abilities to induce cellular stress and toxicity, while others seem to be more potent in propagating neurodegeneration. The preference for particular types of polymorphs depends on the solution conditions and the cellular microenvironment that the protein encounters, which is likely related to the distinct cellular locations of α-synuclein inclusions in different synucleinopathies, and the existence of disease-specific amyloid polymorphs. In this review, we discuss our current understanding on the nature and structure of the various types of α-synuclein aggregated species and their possible roles in pathology. Precisely defining these distinct α-synuclein species will contribute to understanding the molecular origins of these disorders, developing accurate diagnoses, and designing effective therapeutic interventions for these highly debilitating neurodegenerative diseases.
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Affiliation(s)
- Pablo Gracia
- Joint Unit BIFI-IQFR (CSIC), Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain; (P.G.); (J.D.C.)
| | - José D. Camino
- Joint Unit BIFI-IQFR (CSIC), Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain; (P.G.); (J.D.C.)
| | - Laura Volpicelli-Daley
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Nunilo Cremades
- Joint Unit BIFI-IQFR (CSIC), Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, 50018 Zaragoza, Spain; (P.G.); (J.D.C.)
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21
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Madhumitha D, Vaidyanathan V, Dhathathreyan A. Plasticity or elasticity? Relating elastic moduli with secondary structural features of mixed films of polypeptides at air/fluid and fluid/solid interfaces. Biophys Chem 2020; 258:106329. [DOI: 10.1016/j.bpc.2020.106329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 12/11/2022]
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22
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Yarawsky AE, Johns SL, Schuck P, Herr AB. The biofilm adhesion protein Aap from Staphylococcus epidermidis forms zinc-dependent amyloid fibers. J Biol Chem 2020; 295:4411-4427. [PMID: 32102851 DOI: 10.1074/jbc.ra119.010874] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/23/2020] [Indexed: 12/17/2022] Open
Abstract
The skin-colonizing commensal bacterium Staphylococcus epidermidis is a leading cause of hospital-acquired and device-related infections. Its pathogenicity in humans is largely due to its propensity to form biofilms, surface-adherent bacterial accumulations that are remarkably resistant to chemical and physical stresses. Accumulation-associated protein (Aap) from S. epidermidis has been shown to be necessary and sufficient for mature biofilm formation and catheter infection. Aap contains up to 17 tandem B-repeat domains, capable of zinc-dependent assembly into twisted, rope-like intercellular filaments in the biofilm. Using microscopic and biophysical techniques, we show here that Aap B-repeat constructs assemble further into zinc-dependent functional amyloid fibers. We observed such amyloid fibers by confocal microscopy during both early and late stages of S. epidermidis biofilm formation, and we confirmed that extracellular fibrils from these biofilms contain Aap. Unlike what has been observed for amyloidogenic biofilm proteins from other bacteria, which typically use chaperones or initiator proteins to initiate amyloid assembly, our findings indicate that Aap from S. epidermidis requires Zn2+ as a catalyst that drives amyloid fiber formation, similar to many mammalian amyloid-forming proteins that require metals for assembly. This work provides detailed insights into S. epidermidis biofilm formation and architecture that improve our understanding of persistent staphylococcal infections.
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Affiliation(s)
- Alexander E Yarawsky
- Graduate Program in Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
| | - Stefanie L Johns
- Graduate Program in Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Bioengineering, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20814
| | - Andrew B Herr
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229 .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229.,Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
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23
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Cryo-EM structure and polymorphism of Aβ amyloid fibrils purified from Alzheimer's brain tissue. Nat Commun 2019; 10:4760. [PMID: 31664019 PMCID: PMC6820800 DOI: 10.1038/s41467-019-12683-8] [Citation(s) in RCA: 364] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
The formation of Aβ amyloid fibrils is a neuropathological hallmark of Alzheimer's disease and cerebral amyloid angiopathy. However, the structure of Aβ amyloid fibrils from brain tissue is poorly understood. Here we report the purification of Aβ amyloid fibrils from meningeal Alzheimer's brain tissue and their structural analysis with cryo-electron microscopy. We show that these fibrils are polymorphic but consist of similarly structured protofilaments. Brain derived Aβ amyloid fibrils are right-hand twisted and their peptide fold differs sharply from previously analyzed Aβ fibrils that were formed in vitro. These data underscore the importance to use patient-derived amyloid fibrils when investigating the structural basis of the disease.
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24
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Huang YW, King CY. A complete catalog of wild-type Sup35 prion variants and their protein-only propagation. Curr Genet 2019; 66:97-122. [DOI: 10.1007/s00294-019-01003-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/28/2019] [Accepted: 06/01/2019] [Indexed: 10/26/2022]
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25
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Van Acker ZP, Bretou M, Annaert W. Endo-lysosomal dysregulations and late-onset Alzheimer's disease: impact of genetic risk factors. Mol Neurodegener 2019; 14:20. [PMID: 31159836 PMCID: PMC6547588 DOI: 10.1186/s13024-019-0323-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/10/2019] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence supports that cellular dysregulations in the degradative routes contribute to the initiation and progression of neurodegenerative diseases, including Alzheimer's disease. Autophagy and endolysosomal homeostasis need to be maintained throughout life as they are major cellular mechanisms involved in both the production of toxic amyloid peptides and the clearance of misfolded or aggregated proteins. As such, alterations in endolysosomal and autophagic flux, as a measure of degradation activity in these routes or compartments, may directly impact as well on disease-related mechanisms such as amyloid-β clearance through the blood-brain-barrier and the interneuronal spreading of amyloid-β and/or Tau seeds, affecting synaptic function, plasticity and metabolism. The emerging of several genetic risk factors for late-onset Alzheimer's disease that are functionally related to endocytic transport regulation, including cholesterol metabolism and clearance, supports the notion that in particular the autophagy/lysosomal flux might become more vulnerable during ageing thereby contributing to disease onset. In this review we discuss our current knowledge of the risk genes APOE4, BIN1, CD2AP, PICALM, PLD3 and TREM2 and their impact on endolysosomal (dys)regulations in the light of late-onset Alzheimer's disease pathology.
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Affiliation(s)
- Zoë P. Van Acker
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
| | - Marine Bretou
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain & Disease Research, 3000 Leuven, Belgium
- Department of Neurosciences, KU Leuven, Gasthuisberg, O&N4, Rm. 7.159, Herestraat 49, B-3000 Leuven, Belgium
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26
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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27
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Amino acid conformations control the morphological and chiral features of the self-assembled peptide nanostructures: Young investigators perspective. J Colloid Interface Sci 2019; 548:244-254. [PMID: 31004957 DOI: 10.1016/j.jcis.2019.04.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 01/11/2023]
Abstract
HYPOTHESIS A variety of nanostructures with different chiral features can be self-assembled from short peptides with highly similar sequences. We hypothesize that these supramolecular nanostructures are ruled by the constituent amino acid residues which adopt their conformations under the influence of intra-/inter-molecular interactions during peptide self-assembly. APPROACH Through reviewing recent advances in the self-assembly of short peptides and focusing on the relationship between amino acid conformations, peptide secondary structures and intra-/inter-molecular interactions within the supramolecular architectures, we aim to rationalize the complex interactive processes involved in the self-assembly of short, designed peptides. RESULTS Given the highly complexing interactive processes, the adoption of amino acid conformations and their control over peptide self-assembly consist of 4 main steps: (1) Each amino acid residue adopts its unique conformation in a specific sequence; (2) The sequence exhibits its own main chain geometry and determines the propensity of the intermolecular alignment within the building block; (3) The structural propensity of the building block and the packing mode between them determine the self-assembled structural features such as twisting, growth and chirality; (4) In addition to intra-/inter-molecular interactions, inter-sheet and inter-building block interactions could also affect the residue conformations and nanostructures, causing structural readjustment.
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28
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Zheng Y, Xu M, Yu L, Qu F, Lin Y, Xu J, Zou Y, Yang Y, Wang C. Identifying Terminal Assembly Propensity of Amyloidal Peptides by Scanning Tunneling Microscopy. Chemphyschem 2018; 20:103-107. [PMID: 30467942 DOI: 10.1002/cphc.201800975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/21/2018] [Indexed: 11/09/2022]
Abstract
The abnormal accumulation of beta-amyloids (Aβ) in brain is considered as a key initiating cause for Alzheimer's disease (AD) due to their richness in plaques and self-aggregate propensity. In recent studies, N-terminally extended Aβ peptides (NTE-Aβ) with the N-terminus originating prior to the canonical β-secretase cleavage site were found in humans and suggested to have possible relevance to AD. However, the effects of the extended N-terminus on the amyloidegenic structure and aggregation propensity have not been fully elucidated. Herein, we characterized the assembly structures of Aβ1-42, Aβ(-5)-42, Aβ(-10)-42 and Aβ(-15)-42 with both normal and reversed sequences on highly oriented pyrolytic graphite (HOPG) surfaces with scanning tunneling microscopy (STM). The molecularly resolved surface-mediated peptide assemblies enable identification of amyloidegenic fragments. The observations reveal that the assembly propensity of the C-terminal strand of Aβ1-42 is highly conserved and insensitive to N-terminal extensions. In contrast, different assembly structures of the N-terminal strand of Aβ variants can be observed with possible assignment of varied amyloidegenic fragments in the extended N-termini, which may contribute to the varied aggregation propensities of Aβ42 species.
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Affiliation(s)
- Yongfang Zheng
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China.,Department of Chemistry, Tsinghua University, No. 30 ShuangqingRoad, 100084, Beijing, P.R. China
| | - Meng Xu
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China
| | - Lanlan Yu
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China.,Department of Chemistry, Tsinghua University, No. 30 ShuangqingRoad, 100084, Beijing, P.R. China
| | - Fuyang Qu
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China
| | - Yuchen Lin
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China
| | - Jing Xu
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China
| | - Yimin Zou
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China
| | - Yanlian Yang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China
| | - Chen Wang
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, No. 11 ZhongGuanCun BeiYiTiao, 100190, Beijing, P.R. China.,University of the Chinese Academy of Sciences, No. 19 A YuquanRoad, Shijingshan District, 100049, Beijing, P.R. China.,CAS Center for Excellence in Brain Science and Intelligence Technology, No. 320 YueyangRoad, 200031, Shanghai, P.R. China
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29
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A near atomic-scale view at the composition of amyloid-beta fibrils by atom probe tomography. Sci Rep 2018; 8:17615. [PMID: 30514971 PMCID: PMC6279744 DOI: 10.1038/s41598-018-36110-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/05/2018] [Indexed: 01/03/2023] Open
Abstract
Amyloid-beta (Ab) proteins play an important role in a number of neurodegenerative diseases. Ab is found in senile plaques in brains of Alzeimer’s disease patients. The 42 residues of the monomer form dimers which stack to fibrils gaining several micrometers in length. Using Ab fibrils with 13C and 15N marker substitution, we developed an innovative approach to obtain insights to structural and chemical information of the protein. We deposited the modified protein fibrils to pre-sharped aluminium needles with >100-nm apex diameters and, using the position-sensitive mass-to-charge spectrometry technique of atom probe tomography, we acquired the chemically-resolved three dimensional information for every detected ion evaporated in small fragments from the protein. We also discuss the influence of experimental parameters such as pulse energy and pulse frequency of the used Laser beam which lead to differences in the size of the gained fragments, developing the capability of localising metal atom within Ab plaques.
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30
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Alzheimer's Aβ
1‐40
peptide degradation by thermolysin: evidence of inhibition by a C‐terminal Aβ product. FEBS Lett 2018; 593:128-137. [DOI: 10.1002/1873-3468.13285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/18/2018] [Accepted: 10/30/2018] [Indexed: 01/23/2023]
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31
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Galzitskaya OV, Surin AK, Glyakina AV, Rogachevsky VV, Selivanova OM. Should the Treatment of Amyloidosis Be Personified? Molecular Mechanism of Amyloid Formation by Aβ Peptide and Its Fragments. J Alzheimers Dis Rep 2018; 2:181-199. [PMID: 30480261 PMCID: PMC6218156 DOI: 10.3233/adr-180063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Aβ40 and Aβ42 peptides are believed to be associated with Alzheimer's disease. Aggregates (plaques) of Aβ fibrils are found in the brains of humans affected with this disease. The mechanism of formation of Aβ fibrils has not been studied completely, which hinders the development of a correct strategy for therapeutic prevention of this neurodegenerative disorder. It has been found that the most toxic samples upon generation of fibrils are different oligomeric formations. Based on different research methods used for studying amyloidogenesis of Aβ40 and Aβ42 peptides and its amyloidogenic fragments, we have proposed a new mechanism of formation of amyloid fibrils. In accord with this mechanism, the main building unit for fibril generation is a ring-like oligomer. Association of ring-like oligomers results in the formation of fibrils of different morphologies. Our model implies that to prevent development of Alzheimer's disease a therapeutic intervention is required at the earliest stages of amyloidogenesis-at the stage of formation of ring-like oligomers. Therefore, the possibility of a personified approach for prevention not only of Alzheimer's disease development but also of other neurodegenerative diseases associated with the formation of fibrils is argued.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia.,State Scientific Center of Applied Microbiology and Biotechnology, Moscow Region, Serpukhov District, Obolensk, Russia.,Gamaleya Research Center of Epidemiology and Microbiology, Moscow, Russia
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia.,Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Vadim V Rogachevsky
- Institute of Cell Biophysics, Russian Academy of Science, Pushchino, Moscow Region, Russia
| | - Olga M Selivanova
- Institute of Protein Research, Russian Academy of Science, Pushchino, Moscow Region, Russia
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32
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Press-Sandler O, Miller Y. Molecular mechanisms of membrane-associated amyloid aggregation: Computational perspective and challenges. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1889-1905. [DOI: 10.1016/j.bbamem.2018.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 01/02/2023]
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33
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Ilie IM, Caflisch A. Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study. J Phys Chem B 2018; 122:11072-11082. [PMID: 29965774 DOI: 10.1021/acs.jpcb.8b05236] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present a simulation study of the early events of peptide dissociation from a fibril of the Alzheimer's Aβ42 peptide. The fibril consists of layers of two adjacent Aβ42 peptides each folded in an S-shaped structure which has been determined by solid state NMR spectroscopy of a monomorphic disease-relevant species. Multiple molecular dynamics runs (16 at 310 K and 15 at 370 K) were carried out starting from an 18-peptide protofibril for a cumulative sampling of about 15 μs. The simulations show structural stability of the fibrillar core and an overall increase in the twist to about 3 degrees. The N-terminal segment 1-14 is disordered in all peptides. At both ends of the fibril, the central segment 21-29, which includes part of the β2 strand, dissociates in some of the simulations. The β1 and β3 strands, residues 15-20 and 35-41, respectively, are structurally stable. The transient binding of the N-terminal stretch to the β3 strand of the adjacent peptide at the tip is likely to contribute to the arrest phase of the stop-and-go mechanism.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry , University of Zürich , 8057 Zürich , Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry , University of Zürich , 8057 Zürich , Switzerland
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34
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Lee CT, Terentjev EM. Mechanisms and rates of nucleation of amyloid fibrils. J Chem Phys 2018; 147:105103. [PMID: 28915747 DOI: 10.1063/1.4995255] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the "critical nucleus size," nc. The implicit assumption, that amyloids nucleate in the same way, has been recently challenged by an alternative two-step mechanism, when the soluble monomers first form a metastable aggregate (micelle) and then undergo conversion into the conformation rich in β-strands that are able to form a stable growing nucleus for the protofilament. Here we put together the elements of extensive knowledge about aggregation and nucleation kinetics, using a specific case of Aβ1-42 amyloidogenic peptide for illustration, to find theoretical expressions for the effective rate of amyloid nucleation. We find that at low monomer concentrations in solution and also at low interaction energy between two peptide conformations in the micelle, the nucleation occurs via the classical route. At higher monomer concentrations, and a range of other interaction parameters between peptides, the two-step "aggregation-conversion" mechanism of nucleation takes over. In this regime, the effective rate of the process can be interpreted as a power of monomer concentration in a certain range of parameters; however, the exponent is determined by a complicated interplay of interaction parameters and is not related to the minimum size of the growing nucleus (which we find to be ∼7-8 for Aβ1-42).
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Affiliation(s)
- Cheng-Tai Lee
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Eugene M Terentjev
- Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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35
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Galzitskaya OV, Galushko EI, Selivanova OM. Studies of the Process of Amyloid Formation by Aβ Peptide. BIOCHEMISTRY (MOSCOW) 2018; 83:S62-S80. [PMID: 29544432 DOI: 10.1134/s0006297918140079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Studies of the process of amyloid formation by Aβ peptide have been topical due to the critical role of this peptide in the pathogenesis of Alzheimer's disease. Many articles devoted to this process are available in the literature; however, none of them gives a detailed description of the mechanism of the process of generation of amyloids. Moreover, there are no reliable data on the influence of modified forms of Aβ peptide on its amyloid formation. To appreciate the role of Aβ aggregation in the pathogenesis of Alzheimer's disease and to develop a strategy for its treatment, it is necessary to have a well-defined description of the molecular mechanism underlying the formation of amyloids as well as the contribution of each intermediate to this process. We are convinced that a combined analysis of theoretical and experimental methods is a way for understanding molecular mechanisms of numerous diseases. Based on our experimental data and molecular modeling, we have constructed a general model of the process of amyloid formation by Aβ peptide. Using the data described in our previous publications, we propose a model of amyloid formation by this peptide that differs from the generally accepted model. Our model can be applied to other proteins and peptides as well. According to this model, the main building unit for the formation of amyloid fibrils is a ring-like oligomer. Upon interaction with each other, ring-like oligomers form long fibrils of different morphology. This mechanism of generation of amyloid fibrils may be common for other proteins and peptides.
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Affiliation(s)
- O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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36
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Markx D, Loos C, Claus S, Haupt C, Mawrin C, Fändrich M. Cell model for the identification and characterization of prion-like components from Alzheimer brain tissue. Biochem Biophys Res Commun 2018; 497:857-862. [PMID: 29458025 DOI: 10.1016/j.bbrc.2018.02.137] [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: 02/09/2018] [Accepted: 02/15/2018] [Indexed: 11/27/2022]
Abstract
Intracerebral injection of brain extracts from Alzheimer's disease (AD) patients into appropriate mouse models was previously found to drastically accelerate the deposition of Aβ amyloid in the recipient animals indicating a prion-like activity. In this study we show that this prion-like activity can be also identified by using a cell culture model of Aβ plaque formation. Analysis of biochemical fractions of AD brain extract indicate that the seeding-activity correlated with the presence of Aβ peptide and Aβ-derived aggregates. In vitro-formed fibrils were also active but their activity was low and depending on the fibril structure and conditions of fibril formation. Our data indicate a conformational basis of the observed seeding effect and suggest the utility of our cell model for further studies on the prion-like activity of AD extracts.
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Affiliation(s)
- Daniel Markx
- Institute of Protein Biochemistry, Ulm University, Helmholtzstr. 8/1, 89081 Ulm, Germany
| | - Cornelia Loos
- Institute of Protein Biochemistry, Ulm University, Helmholtzstr. 8/1, 89081 Ulm, Germany
| | - Stephanie Claus
- Institute of Protein Biochemistry, Ulm University, Helmholtzstr. 8/1, 89081 Ulm, Germany
| | - Christian Haupt
- Institute of Protein Biochemistry, Ulm University, Helmholtzstr. 8/1, 89081 Ulm, Germany
| | - Christian Mawrin
- Institute of Neuropathology, Otto-von-Guericke University, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Helmholtzstr. 8/1, 89081 Ulm, Germany.
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37
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Kulawik A, Heise H, Zafiu C, Willbold D, Bannach O. Advancements of the
sFIDA
method for oligomer‐based diagnostics of neurodegenerative diseases. FEBS Lett 2018; 592:516-534. [DOI: 10.1002/1873-3468.12983] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Andreas Kulawik
- Institute of Complex Systems (ICS‐6: Structural Biochemistry) Forschungszentrum Jülich Germany
- Institut für Physikalische Biologie Heinrich‐Heine‐Universität Düsseldorf Germany
| | - Henrike Heise
- Institute of Complex Systems (ICS‐6: Structural Biochemistry) Forschungszentrum Jülich Germany
- Institut für Physikalische Biologie Heinrich‐Heine‐Universität Düsseldorf Germany
| | - Christian Zafiu
- Institute of Complex Systems (ICS‐6: Structural Biochemistry) Forschungszentrum Jülich Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS‐6: Structural Biochemistry) Forschungszentrum Jülich Germany
- Institut für Physikalische Biologie Heinrich‐Heine‐Universität Düsseldorf Germany
| | - Oliver Bannach
- Institute of Complex Systems (ICS‐6: Structural Biochemistry) Forschungszentrum Jülich Germany
- Institut für Physikalische Biologie Heinrich‐Heine‐Universität Düsseldorf Germany
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38
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Selivanova OM, Surin AK, Marchenkov VV, Dzhus UF, Grigorashvili EI, Suvorina MY, Glyakina AV, Dovidchenko NV, Galzitskaya OV. The Mechanism Underlying Amyloid Polymorphism is Opened for Alzheimer's Disease Amyloid-β Peptide. J Alzheimers Dis 2018; 54:821-30. [PMID: 27567850 DOI: 10.3233/jad-160405] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
It has been demonstrated using Aβ40 and Aβ42 recombinant and synthetic peptides that their fibrils are formed of complete oligomer ring structures. Such ring structures have a diameter of about 8-9 nm, an oligomer height of about 2- 4 nm, and an internal diameter of the ring of about 3-4 nm. Oligomers associate in a fibril in such a way that they interact with each other, overlapping slightly. There are differences in the packing of oligomers in fibrils of recombinant and synthetic Aβ peptides. The principal difference is in the degree of orderliness of ring-like oligomers that leads to generation of morphologically different fibrils. Most ordered association of ring-like structured oligomers is observed for a recombinant Aβ40 peptide. Less ordered fibrils are observed with the synthetic Aβ42 peptide. Fragments of fibrils the most protected from the action of proteases have been determined by tandem mass spectrometry. It was shown that unlike Aβ40, fibrils of Aβ42 are more protected, showing less ordered organization compared to that of Aβ40 fibrils. Thus, the mass spectrometry data agree with the electron microscopy data and structural models presented here.
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Affiliation(s)
- Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov District, Moscow Region, Russia
| | - Victor V Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Ulyana F Dzhus
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Mariya Yu Suvorina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Institute of Mathematical Problems of Biology, Pushchino, Moscow Region, Russia
| | - Nikita V Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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39
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Huang D, Hudson BC, Gao Y, Roberts EK, Paravastu AK. Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels. Methods Mol Biol 2018; 1777:23-68. [PMID: 29744827 PMCID: PMC7490753 DOI: 10.1007/978-1-4939-7811-3_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] [Indexed: 02/17/2023]
Abstract
For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin-spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.
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Affiliation(s)
- Danting Huang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Benjamin C Hudson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Evan K Roberts
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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40
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Giri RS, Mandal B. Boc-Val-Val-OMe (Aβ39–40) and Boc-Ile-Ala-OMe (Aβ41–42) crystallize in a parallel β-sheet arrangement but generate a different morphology. CrystEngComm 2018. [DOI: 10.1039/c8ce00097b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Crystal structures and morphologies of Boc-Val-Val-OMe (Aβ39–40) and Boc-Ile-Ala-OMe (Aβ41–42), the two consecutive dipeptides of the C-terminus of Aβ, are reported.
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Affiliation(s)
- Rajat Subhra Giri
- Department of Chemistry
- Laboratory of Peptide and Amyloid Research
- Indian Institute of Technology Guwahati
- India
| | - Bhubaneswar Mandal
- Department of Chemistry
- Laboratory of Peptide and Amyloid Research
- Indian Institute of Technology Guwahati
- India
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41
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Abstract
Amyloid assemblies of certain proteins, including the Parkinson disease-related protein α-synuclein, are commonly associated with the development and spreading of neurodegenerative diseases, although the nature of the most toxic forms and the mechanisms by which they trigger neurodegeneration remain largely unknown. This is at least in part due to the inherent challenges involved in the preparation of stable and structurally homogeneous samples of amyloid assemblies that could be used in toxicity experiments. Here, we describe the preparation of two different types of stable α-synuclein amyloid assemblies, namely a kinetically trapped oligomeric species and a propagating-competent fibrillar polymorph. The degree of heterogeneity in the samples has been defined and carefully minimized, thus allowing for meaningful structure-toxicity relationships in different α-synuclein amyloid assemblies to be established.
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42
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Pollock-Gagolashvili M, Miller Y. Two Distinct Polymorphic Folding States of Self-Assembly of the Non-amyloid-β Component Differ in the Arrangement of the Residues. ACS Chem Neurosci 2017; 8:2613-2617. [PMID: 28914525 DOI: 10.1021/acschemneuro.7b00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Parkinson's disease is a degenerative disorder of the central nervous system. It is characterized by presence of Lewy bodies (LBs), in which the main components of the LBs are α-synuclein (AS) aggregates. The central domain of AS, known as the "non-amyloid-β component" (NAC) is responsible for the aggregation properties of AS. It is proposed that AS fibrillar structure is a well-packed cross-β structure of the NAC domains, while the N- and C-termini are disordered. Therefore, the study of the self-assembly of NAC domains is crucial in order to understand the molecular mechanisms of AS aggregation. This is a first study that illustrates two distinct polymorphic folding states of NAC that differ in the arrangement of the residues along the sequence. One of the polymorphic folding states reveals a conformational change that is similar to the other polymorphic folding state in the backbone shape but differs in the arrangement of the residues along the backbone. This work provides insight into the molecular mechanisms through which AS can self-assembled in two different pathways yielding a conformational change between the two polymorphic folding states.
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Affiliation(s)
- Maya Pollock-Gagolashvili
- Department
of Chemistry and ‡Ilse Katz Institute for Nanoscale Science
and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Miller
- Department
of Chemistry and ‡Ilse Katz Institute for Nanoscale Science
and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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43
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Ochalek A, Mihalik B, Avci HX, Chandrasekaran A, Téglási A, Bock I, Giudice ML, Táncos Z, Molnár K, László L, Nielsen JE, Holst B, Freude K, Hyttel P, Kobolák J, Dinnyés A. Neurons derived from sporadic Alzheimer's disease iPSCs reveal elevated TAU hyperphosphorylation, increased amyloid levels, and GSK3B activation. ALZHEIMERS RESEARCH & THERAPY 2017; 9:90. [PMID: 29191219 PMCID: PMC5709977 DOI: 10.1186/s13195-017-0317-z] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common type of dementia, affecting one in eight adults over 65 years of age. The majority of AD cases are sporadic, with unknown etiology, and only 5% of all patients with AD present the familial monogenic form of the disease. In the present study, our aim was to establish an in vitro cell model based on patient-specific human neurons to study the pathomechanism of sporadic AD. METHODS We compared neurons derived from induced pluripotent stem cell (iPSC) lines of patients with early-onset familial Alzheimer's disease (fAD), all caused by mutations in the PSEN1 gene; patients with late-onset sporadic Alzheimer's disease (sAD); and three control individuals without dementia. The iPSC lines were differentiated toward mature cortical neurons, and AD pathological hallmarks were analyzed by RT-qPCR, enzyme-linked immunosorbent assay, and Western blotting methods. RESULTS Neurons from patients with fAD and patients with sAD showed increased phosphorylation of TAU protein at all investigated phosphorylation sites. Relative to the control neurons, neurons derived from patients with fAD and patients with sAD exhibited higher levels of extracellular amyloid-β 1-40 (Aβ1-40) and amyloid-β 1-42 (Aβ1-42). However, significantly increased Aβ1-42/Aβ1-40 ratios, which is one of the pathological markers of fAD, were observed only in samples of patients with fAD. Additionally, we detected increased levels of active glycogen synthase kinase 3 β, a physiological kinase of TAU, in neurons derived from AD iPSCs, as well as significant upregulation of amyloid precursor protein (APP) synthesis and APP carboxy-terminal fragment cleavage. Moreover, elevated sensitivity to oxidative stress, as induced by amyloid oligomers or peroxide, was detected in both fAD- and sAD-derived neurons. CONCLUSIONS On the basis of the experiments we performed, we can conclude there is no evident difference except secreted Aβ1-40 levels in phenotype between fAD and sAD samples. To our knowledge, this is the first study in which the hyperphosphorylation of TAU protein has been compared in fAD and sAD iPSC-derived neurons. Our findings demonstrate that iPSC technology is suitable to model both fAD and sAD and may provide a platform for developing new treatment strategies for these conditions.
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Affiliation(s)
- Anna Ochalek
- Molecular Animal Biotechnology Laboratory, Szent István University, H-2100, Gödöllő, Hungary.,BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary
| | - Balázs Mihalik
- BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary
| | - Hasan X Avci
- BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary.,Department of Anatomy, Embryology and Histology, Faculty of Medicine, University of Szeged, H-6700, Szeged, Hungary.,Present address: University Department of Otolaryngology, Head and Neck Surgery, University of Tübingen, 72076, Tübingen, Germany
| | | | | | - István Bock
- BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary
| | - Maria Lo Giudice
- BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary
| | - Zsuzsanna Táncos
- BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary
| | - Kinga Molnár
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - Lajos László
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - Jørgen E Nielsen
- Neurogenetics Clinic & Research Laboratory, Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Kristine Freude
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Copenhagen, Denmark
| | - Poul Hyttel
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870, Copenhagen, Denmark
| | - Julianna Kobolák
- BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary
| | - András Dinnyés
- Molecular Animal Biotechnology Laboratory, Szent István University, H-2100, Gödöllő, Hungary. .,BioTalentum Ltd., Aulich Lajos Street 26, H-2100, Gödöllő, Hungary.
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44
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Bacci M, Vymětal J, Mihajlovic M, Caflisch A, Vitalis A. Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. J Chem Theory Comput 2017; 13:5117-5130. [PMID: 28870064 DOI: 10.1021/acs.jctc.7b00662] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The growth of amyloid fibrils from Aβ1-42 peptide, one of the key pathogenic players in Alzheimer's disease, is believed to follow a nucleation-elongation mechanism. Fibril elongation is often described as a "dock-lock" procedure, where a disordered monomer adsorbs to an existing fibril in a relatively fast process (docking), followed by a slower conformational transition toward the ordered state of the template (locking). Here, we use molecular dynamics simulations of an ordered pentamer of Aβ42 at fully atomistic resolution, which includes solvent, to characterize the elongation process. We construct a Markov state model from an ensemble of short trajectories generated by an advanced sampling algorithm that efficiently diversifies a subset of the system without any bias forces. This subset corresponds to selected dihedral angles of the peptide chain at the fibril tip favored to be the fast growing one experimentally. From the network model, we extract distinct locking pathways covering time scales in the high microsecond regime. Slow steps are associated with the exchange of hydrophobic contacts, between nonnative and native intermolecular contacts as well as between intra- and intermolecular ones. The N-terminal segments, which are disordered in fibrils and typically considered inert, are able to shield the lateral interfaces of the pentamer. We conclude by discussing our findings in the context of a refined dock-lock model of Aβ fibril elongation, which involves structural disorder for more than one monomer at the growing tip.
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Affiliation(s)
- Marco Bacci
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jiří Vymětal
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Maja Mihajlovic
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- University of Zurich , Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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45
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Kushida S, Oki O, Saito H, Kuwabara J, Kanbara T, Tashiro M, Katouda M, Imamura Y, Yamamoto Y. From Linear to Foldamer and Assembly: Hierarchical Transformation of a Coplanar Conjugated Polymer into a Microsphere. J Phys Chem Lett 2017; 8:4580-4586. [PMID: 28880560 DOI: 10.1021/acs.jpclett.7b02102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Despite the coplanar structure, a conjugated alternating copolymer forms amorphous, well-defined microspheres without π-stacked crystalline domains. Here, we gain insights into the mechanism of how the coplanar conjugated polymer forms amorphous microspheres by means of spectroscopic studies on the assembly/disassembly processes. The difference of the spectral profiles of photoabsorption and photoluminescence with varying solvent/nonsolvent composition clarifies that stepwise assembly takes place through the microsphere formation; [1] intrapolymer linear-to-folding transformation upon diffusion of polar nonsolvent and [2] interpolymer assembly of the foldamers upon further addition of the nonsolvent to form microspheres. As shown in various biopolymers such as proteins and DNA, such stepwise folding and assembly behaviors of conjugated polymers from primary to secondary and tertiary structure open a new way to create transformable functional materials.
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Affiliation(s)
| | | | | | | | | | - Motomichi Tashiro
- Department of Applied Chemistry, Toyo University , Kujirai 2100, Kawagoe, Saitama 350-8585, Japan
| | - Michio Katouda
- Advanced Institute for Computational Science, RIKEN , 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yutaka Imamura
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University , 1-1 minami-Osawa, Hachioji, Tokyo 192-0397, Japan
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46
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Silvers R, Colvin MT, Frederick KK, Jacavone AC, Lindquist S, Linse S, Griffin RG. Aggregation and Fibril Structure of Aβ M01-42 and Aβ 1-42. Biochemistry 2017; 56:4850-4859. [PMID: 28792214 PMCID: PMC8254419 DOI: 10.1021/acs.biochem.7b00729] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A mechanistic understanding of Aβ aggregation and high-resolution structures of Aβ fibrils and oligomers are vital to elucidating relevant details of neurodegeneration in Alzheimer's disease, which will facilitate the rational design of diagnostic and therapeutic protocols. The most detailed and reproducible insights into structure and kinetics have been achieved using Aβ peptides produced by recombinant expression, which results in an additional methionine at the N-terminus. While the length of the C-terminus is well established to have a profound impact on the peptide's aggregation propensity, structure, and neurotoxicity, the impact of the N-terminal methionine on the aggregation pathways and structure is unclear. For this reason, we have developed a protocol to produce recombinant Aβ1-42, sans the N-terminal methionine, using an N-terminal small ubiquitin-like modifier-Aβ1-42 fusion protein in reasonable yield, with which we compared aggregation kinetics with AβM01-42 containing the additional methionine residue. The data revealed that Aβ1-42 and AβM01-42 aggregate with similar rates and by the same mechanism, in which the generation of new aggregates is dominated by secondary nucleation of monomers on the surface of fibrils. We also recorded magic angle spinning nuclear magnetic resonance spectra that demonstrated that excellent spectral resolution is maintained with both AβM01-42 and Aβ1-42 and that the chemical shifts are virtually identical in dipolar recoupling experiments that provide information about rigid residues. Collectively, these results indicate that the structure of the fibril core is unaffected by N-terminal methionine. This is consistent with the recent structures of AβM01-42 in which M0 is located at the terminus of a disordered 14-amino acid N-terminal tail.
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Affiliation(s)
- Robert Silvers
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Michael T Colvin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Kendra K Frederick
- Whitehead Institute for Biomedical Research , Nine Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Angela C Jacavone
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research , Nine Cambridge Center, Cambridge, Massachusetts 02142, United States
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University , SE22100 Lund, Sweden
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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47
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Gremer L, Schölzel D, Schenk C, Reinartz E, Labahn J, Ravelli RBG, Tusche M, Lopez-Iglesias C, Hoyer W, Heise H, Willbold D, Schröder GF. Fibril structure of amyloid-β(1-42) by cryo-electron microscopy. Science 2017; 358:116-119. [PMID: 28882996 DOI: 10.1126/science.aao2825] [Citation(s) in RCA: 701] [Impact Index Per Article: 100.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/24/2017] [Indexed: 01/02/2023]
Abstract
Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer's disease patients. We present the structure of an Aβ(1-42) fibril composed of two intertwined protofilaments determined by cryo-electron microscopy (cryo-EM) to 4.0-angstrom resolution, complemented by solid-state nuclear magnetic resonance experiments. The backbone of all 42 residues and nearly all side chains are well resolved in the EM density map, including the entire N terminus, which is part of the cross-β structure resulting in an overall "LS"-shaped topology of individual subunits. The dimer interface protects the hydrophobic C termini from the solvent. The characteristic staggering of the nonplanar subunits results in markedly different fibril ends, termed "groove" and "ridge," leading to different binding pathways on both fibril ends, which has implications for fibril growth.
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Affiliation(s)
- Lothar Gremer
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Daniel Schölzel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Carla Schenk
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Elke Reinartz
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Jörg Labahn
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.,Centre for Structural Systems Biology (CSSB), Deutsches Elektronen-Synchrotron (DESY), 22607 Hamburg, Germany
| | - Raimond B G Ravelli
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, Netherlands
| | - Markus Tusche
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Carmen Lopez-Iglesias
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, Netherlands
| | - Wolfgang Hoyer
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Henrike Heise
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany. .,Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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48
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Amyloid-β Peptide Nitrotyrosination Stabilizes Oligomers and Enhances NMDAR-Mediated Toxicity. J Neurosci 2017; 36:11693-11703. [PMID: 27852777 DOI: 10.1523/jneurosci.1081-16.2016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/10/2016] [Accepted: 09/10/2016] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the pathological aggregation of the amyloid-β peptide (Aβ). Monomeric soluble Aβ can switch from helicoidal to β-sheet conformation, promoting its assembly into oligomers and subsequently to amyloid fibrils. Oligomers are highly toxic to neurons and have been reported to induce synaptic transmission impairments. The progression from oligomers to fibrils forming senile plaques is currently considered a protective mechanism to avoid the presence of the highly toxic oligomers. Protein nitration is a frequent post-translational modification under AD nitrative stress conditions. Aβ can be nitrated at tyrosine 10 (Y10) by peroxynitrite. Based on our analysis of ThT binding, Western blot and electron and atomic force microscopy, we report that Aβ nitration stabilizes soluble, highly toxic oligomers and impairs the formation of fibrils. We propose a mechanism by which fibril elongation is interrupted upon Y10 nitration: Nitration disrupts fibril-forming folds by preventing H14-mediated bridging, as shown with an Aβ analog containing a single residue (H to E) replacement that mimics the behavior of nitrated Aβ related to fibril formation and neuronal toxicity. The pathophysiological role of our findings in AD was highlighted by the study of these nitrated oligomers on mouse hippocampal neurons, where an increased NMDAR-dependent toxicity of nitrated Aβ oligomers was observed. Our results show that Aβ nitrotyrosination is a post-translational modification that increases Aβ synaptotoxicity. SIGNIFICANCE STATEMENT We report that nitration (i.e., the irreversible addition of a nitro group) of the Alzheimer-related peptide amyloid-β (Aβ) favors the stabilization of highly toxic oligomers and inhibits the formation of Aβ fibrils. The nitrated Aβ oligomers are more toxic to neurons due to increased cytosolic calcium levels throughout their action on NMDA receptors. Sustained elevated calcium levels trigger excitotoxicity, a characteristic event in Alzheimer's disease.
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49
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Cremades N, Dobson CM. The contribution of biophysical and structural studies of protein self-assembly to the design of therapeutic strategies for amyloid diseases. Neurobiol Dis 2017; 109:178-190. [PMID: 28709995 DOI: 10.1016/j.nbd.2017.07.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/26/2017] [Accepted: 07/10/2017] [Indexed: 01/26/2023] Open
Abstract
Many neurodegenerative disorders, including Alzheimer's, Parkinson's and the prion diseases, are characterized by a conformational conversion of normally soluble proteins or peptides into pathological species, by a process of misfolding and self-assembly that leads ultimately to the formation of amyloid fibrils. Recent studies support the idea that multiple intermediate species with a wide variety of degrees of neuronal toxicity are generated during such processes. The development of a high level of knowledge of the nature and structure of the pathogenic amyloid species would significantly enhance efforts to underline the molecular origins of these disorders and also to develop both accurate diagnoses and effective therapeutic interventions for these types of conditions. In this review, we discuss recent biophysical and structural information concerning different types of amyloid aggregates and the way in which such information can guide rational therapeutic approaches designed to target specific pathogenic events that occur during the development of these highly debilitating and increasingly common diseases.
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Affiliation(s)
- Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain.
| | - Christopher M Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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50
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Wang M, Zhou P, Wang J, Zhao Y, Ma H, Lu JR, Xu H. Left or Right: How Does Amino Acid Chirality Affect the Handedness of Nanostructures Self-Assembled from Short Amphiphilic Peptides? J Am Chem Soc 2017; 139:4185-4194. [PMID: 28240550 DOI: 10.1021/jacs.7b00847] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Peptide and protein fibrils have attracted an enormous amount of interests due to their relevance to many neurodegenerative diseases and their potential applications in nanotechnology. Although twisted fibrils are regarded as the key intermediate structures of thick fibrils or bundles of fibrils, the factors determining their twisting tendency and their handedness development from the molecular to the supramolecular level are still poorly understood. In this study, we have designed three pairs of enantiomeric short amphiphilic peptides: LI3LK and DI3DK, LI3DK and DI3LK, and LaI3LK and DaI3DK, and investigated the chirality of their self-assembled nanofibrils through the combined use of atomic force microscopy (AFM), circular dichroism (CD) spectroscopy, scanning electron microscopy (SEM), and molecular dynamic (MD) simulations. The results indicated that the twisted handedness of the supramolecular nanofibrils was dictated by the chirality of the hydrophilic Lys head at the C-terminal, while their characteristic CD signals were determined by the chirality of hydrophobic Ile residues. MD simulations delineated the handedness development from molecular chirality to supramolecular handedness by showing that the β-sheets formed by LI3LK, LaI3LK, and DI3LK exhibited a propensity to twist in a left-handed direction, while the ones of DI3DK, DaI3DK, and LI3DK in a right-handed twisting orientation.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
| | - Hongchao Ma
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
| | - Jian R Lu
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester , Schuster Building, Manchester M13 9PL, U.K
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
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