1
|
Secco V, Tiago T, Staats R, Preet S, Chia S, Vendruscolo M, Carra S. HSPB6: A lipid-dependent molecular chaperone inhibits α-synuclein aggregation. iScience 2024; 27:110657. [PMID: 39280615 PMCID: PMC11402235 DOI: 10.1016/j.isci.2024.110657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/09/2024] [Accepted: 07/31/2024] [Indexed: 09/18/2024] Open
Abstract
The process of protein misfolding and aggregation is associated with various cytotoxic effects. Understanding how this phenomenon is regulated by the protein homeostasis system, however, is difficult, since it takes place through a complex non-linear network of coupled microscopic steps, including primary nucleation, fibril elongation, and secondary nucleation, which depend on environmental factors. To address this problem, we studied how the aggregation of α-synuclein, a protein associated with Parkinson's disease, is modulated by molecular chaperones and lipid membranes. We focused on small heat shock proteins (sHSPs/HSPBs), which interact with proteins and lipids and are upregulated during aging, a major risk factor for protein misfolding diseases. HSPBs act on different microscopic steps to prevent α-synuclein aggregation, with HSPB6 showing a lipid-dependent chaperone activity. Our findings provide an example of how HSPBs diversified their mechanisms of action to reach an efficient regulation of protein misfolding and aggregation within the complex cellular environment.
Collapse
Affiliation(s)
- Valentina Secco
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Tatiana Tiago
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Roxine Staats
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Swapan Preet
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sean Chia
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| |
Collapse
|
2
|
Rout SK, Rhyner D, Greenwald J, Riek R. Characterization of self-templating catalytic amyloids. Methods Enzymol 2024; 697:51-75. [PMID: 38816135 DOI: 10.1016/bs.mie.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Amyloid aggregates with unique periodic structures have garnered significant attention due to their association with numerous diseases, including systemic amyloidoses and the neurodegenerative diseases Parkinson's, Alzheimer's, and Creutzfeld-Jakob. However, more recent investigations have expanded our understanding of amyloids, revealing their diverse functional biological roles. Amyloids have also been proposed to have played a significant role in prebiotic molecular evolution because of their exceptional stability, spontaneous formation in a prebiotic environment, catalytic and templating abilities, and cooperative interaction with fatty acids, polysaccharides, and nucleic acids. This chapter summarizes methods and techniques associated with studying short amyloidogenic peptides, including detailed procedures for investigating cross-templating and autocatalytic templating reactions. Since the work with amyloidogenic peptides and their aggregates present unique challenges, we have attempted to address these with essential details throughout the procedures. The lessons herein may be used in any amyloid-related research to ensure more reproducible results and reduce entrance barriers for researchers new to the field.
Collapse
Affiliation(s)
- Saroj K Rout
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland; Systems Biophysics, Department of Physics, Ludwig Maximilian University Munich, Munich, Germany
| | - David Rhyner
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland
| | - Jason Greenwald
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland.
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
3
|
Das T, Zaidi F, Farag M, Ruff KM, Messing J, Taylor JP, Pappu RV, Mittag T. Metastable condensates suppress conversion to amyloid fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582569. [PMID: 38464104 PMCID: PMC10925303 DOI: 10.1101/2024.02.28.582569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Stress granules form via co-condensation of RNA binding proteins with prion-like low complexity domains (PLCDs) and RNA molecules released by stress-induced polysomal runoff. Homotypic interactions among PLCDs can drive amyloid fibril formation and this is enhanced by ALS-associated mutations. We find that homotypic interactions that drive condensation versus fibril formation are separable for A1-LCD, the PLCD of hnRNPA1. These separable interactions lead to condensates that are metastable versus fibrils that are globally stable. Metastable condensates suppress fibril formation, and ALS-associated mutations enhance fibril formation by weakening condensate metastability. Mutations designed to enhance A1-LCD condensate metastability restore wild-type behaviors of stress granules in cells even when ALS-associated mutations are present. This suggests that fibril formation can be suppressed by enhancing condensate metastability through condensate-driving interactions.
Collapse
Affiliation(s)
- Tapojyoti Das
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Fatima Zaidi
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Mina Farag
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| |
Collapse
|
4
|
James EI, Baggett DW, Chang E, Schachter J, Nixey T, Choi K, Guttman M, Nath A. Tryptanthrin Analogs Substoichiometrically Inhibit Seeded and Unseeded Tau4RD Aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578649. [PMID: 38352474 PMCID: PMC10862865 DOI: 10.1101/2024.02.02.578649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Microtubule-associated protein tau is an intrinsically disordered protein (IDP) that forms characteristic fibrillar aggregates in several diseases, the most well-known of which is Alzheimer's disease (AD). Despite keen interest in disrupting or inhibiting tau aggregation to treat AD and related dementias, there are currently no FDA-approved tau-targeting drugs. This is due, in part, to the fact that tau and other IDPs do not exhibit a single well-defined conformation but instead populate a fluctuating conformational ensemble that precludes finding a stable "druggable" pocket. Despite this challenge, we previously reported the discovery of two novel families of tau ligands, including a class of aggregation inhibitors, identified through a protocol that combines molecular dynamics, structural analysis, and machine learning. Here we extend our exploration of tau druggability with the identification of tryptanthrin and its analogs as potent, substoichiometric aggregation inhibitors, with the best compounds showing potencies in the low nanomolar range even at a ~100-fold molar excess of tau4RD. Moreover, conservative changes in small molecule structure can have large impacts on inhibitory potency, demonstrating that similar structure-activity relationship (SAR) principles as used for traditional drug development also apply to tau and potentially to other IDPs.
Collapse
Affiliation(s)
- Ellie I. James
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
| | - David W. Baggett
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Current address: Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Edcon Chang
- Takeda Development Center Americas, San Diego, CA
| | | | - Thomas Nixey
- Takeda Development Center Americas, San Diego, CA
| | | | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA
| |
Collapse
|
5
|
Gardon L, Becker N, Rähse N, Hölbling C, Apostolidis A, Schulz CM, Bochinsky K, Gremer L, Heise H, Lakomek NA. Amyloid fibril formation kinetics of low-pH denatured bovine PI3K-SH3 monitored by three different NMR techniques. Front Mol Biosci 2023; 10:1254721. [PMID: 38046811 PMCID: PMC10691488 DOI: 10.3389/fmolb.2023.1254721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
Introduction: Misfolding of amyloidogenic proteins is a molecular hallmark of neurodegenerative diseases in humans. A detailed understanding of the underlying molecular mechanisms is mandatory for developing innovative therapeutic approaches. The bovine PI3K-SH3 domain has been a model system for aggregation and fibril formation. Methods: We monitored the fibril formation kinetics of low pH-denatured recombinantly expressed [U-13C, 15N] labeled bovine PI3K-SH3 by a combination of solution NMR, high-resolution magic angle spinning (HR-MAS) NMR and solid-state NMR spectra. Solution NMR offers the highest sensitivity and, therefore, allows for the recording of two-dimensional NMR spectra with residue-specific resolution for individual time points of the time series. However, it can only follow the decay of the aggregating monomeric species. In solution NMR, aggregation occurs under quiescent experimental conditions. Solid-state NMR has lower sensitivity and allows only for the recording of one-dimensional spectra during the time series. Conversely, solid-state NMR is the only technique to detect disappearing monomers and aggregated species in the same sample by alternatingly recoding scalar coupling and dipolar coupling (CP)-based spectra. HR-MAS NMR is used here as a hybrid method bridging solution and solid-state NMR. In solid-state NMR and HR-MAS NMR the sample is agitated due to magic angle spinning. Results: Good agreement of the decay rate constants of monomeric SH3, measured by the three different NMR methods, is observed. Moderate MAS up to 8 kHz seems to influence the aggregation kinetics of seeded fibril formation only slightly. Therefore, under sufficient seeding (1% seeds used here), quiescent conditions (solution NMR), and agitated conditions deliver similar results, arguing against primary nucleation induced by MAS as a major contributor. Using solid-state NMR, we find that the amount of disappeared monomer corresponds approximately to the amount of aggregated species under the applied experimental conditions (250 µM PI3K-SH3, pH 2.5, 298 K, 1% seeds) and within the experimental error range. Data can be fitted by simple mono-exponential conversion kinetics, with lifetimes τ in the 14-38 h range. Atomic force microscopy confirms that fibrils substantially grew in length during the aggregation experiment. This argues for fibril elongation as the dominant growth mechanism in fibril mass (followed by the CP-based solid-state NMR signal). Conclusion: We suggest a combined approach employing both solution NMR and solid-state NMR, back-to-back, on two aliquots of the same sample under seeding conditions as an additional approach to follow monomer depletion and growth of fibril mass simultaneously. Atomic force microscopy images confirm fibril elongation as a major contributor to the increase in fibril mass.
Collapse
Affiliation(s)
- Luis Gardon
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nina Becker
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nick Rähse
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Christoph Hölbling
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Athina Apostolidis
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Celina M. Schulz
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Kevin Bochinsky
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nils-Alexander Lakomek
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
6
|
Paladino A, Vitagliano L, Graziano G. The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins. BIOLOGY 2023; 12:biology12050754. [PMID: 37237566 DOI: 10.3390/biology12050754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.
Collapse
Affiliation(s)
- Antonella Paladino
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, 82100 Benevento, Italy
| |
Collapse
|
7
|
Lyubchenko YL. Protein Self-Assembly at the Liquid-Surface Interface. Surface-Mediated Aggregation Catalysis. J Phys Chem B 2023; 127:1880-1889. [PMID: 36812408 DOI: 10.1021/acs.jpcb.2c09029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Protein self-assembly into aggregates of various morphologies is a ubiquitous phenomenon in physical chemistry and biophysics. The critical role of amyloid assemblies in the development of diseases, neurodegenerative diseases especially, highlights the importance of understanding the mechanistic picture of the self-assembly process. The translation of this knowledge to the development of efficient preventions and treatments for diseases requires designing experiments at conditions mimicking those in vivo. This Perspective reviews data satisfying two major requirements: membrane environment and physiologically low concentrations of proteins. Recent progress in experiments and computational modeling resulted in a novel model for the amyloid aggregation process at the membrane-liquid interface. The self-assembly under such conditions has a number of critical features, further understanding of which can lead to the development of efficient preventive means and treatments for Alzheimer's and other devastating neurodegenerative disorders.
Collapse
Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| |
Collapse
|
8
|
Zhou X, Sinkjær AW, Zhang M, Pinholt HD, Nielsen HM, Hatzakis NS, van de Weert M, Foderà V. Heterogeneous and Surface-Catalyzed Amyloid Aggregation Monitored by Spatially Resolved Fluorescence and Single Molecule Microscopy. J Phys Chem Lett 2023; 14:912-919. [PMID: 36669144 DOI: 10.1021/acs.jpclett.2c03400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Amyloid aggregation is associated with many diseases and may also occur in therapeutic protein formulations. Addition of co-solutes is a key strategy to modulate the stability of proteins in pharmaceutical formulations and select inhibitors for drug design in the context of diseases. However, the heterogeneous nature of this multicomponent system in terms of structures and mechanisms poses a number of challenges for the analysis of the chemical reaction. Using insulin as protein system and polysorbate 80 as co-solute, we combine a spatially resolved fluorescence approach with single molecule microscopy and machine learning methods to kinetically disentangle the different contributions from multiple species within a single aggregation experiment. We link the presence of interfaces to the degree of heterogeneity of the aggregation kinetics and retrieve the rate constants and underlying mechanisms for single aggregation events. Importantly, we report that the mechanism of inhibition of the self-assembly process depends on the details of the growth pathways of otherwise macroscopically identical species. This information can only be accessed by the analysis of single aggregate events, suggesting our method as a general tool for a comprehensive physicochemical characterization of self-assembly reactions.
Collapse
Affiliation(s)
- Xin Zhou
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Anders Wilgaard Sinkjær
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Henrik Dahl Pinholt
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hanne Mørck Nielsen
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Marco van de Weert
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vito Foderà
- Drug Delivery and Biophysics of Biopharmaceuticals and Center for Biopharmaceuticals and Biobarriers in Drug Delivery (BioDelivery), Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen Universitetsparken 5, 2100 Copenhagen, Denmark
| |
Collapse
|
9
|
Estaun-Panzano J, Arotcarena ML, Bezard E. Monitoring α-synuclein aggregation. Neurobiol Dis 2023; 176:105966. [PMID: 36527982 PMCID: PMC9875312 DOI: 10.1016/j.nbd.2022.105966] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Synucleinopathies, including Parkinson's disease (PD), dementia with Lewy Bodies (DLB), and multiple system atrophy (MSA), are characterized by the misfolding and subsequent aggregation of alpha-synuclein (α-syn) that accumulates in cytoplasmic inclusions bodies in the cells of affected brain regions. Since the seminal report of likely-aggregated α-syn presence within the Lewy bodies by Spillantini et al. in 1997, the keyword "synuclein aggregation" has appeared in over 6000 papers (Source: PubMed October 2022). Studying, observing, describing, and quantifying α-syn aggregation is therefore of paramount importance, whether it happens in tubo, in vitro, in post-mortem samples, or in vivo. The past few years have witnessed tremendous progress in understanding aggregation mechanisms and identifying various polymorphs. In this context of growing complexity, it is of utmost importance to understand what tools we possess, what exact information they provide, and in what context they may be applied. Nonetheless, it is also crucial to rationalize the relevance of the information and the limitations of these methods for gauging the final result. In this review, we present the main techniques that have shaped the current views about α-syn structure and dynamics, with particular emphasis on the recent breakthroughs that may change our understanding of synucleinopathies.
Collapse
Affiliation(s)
| | | | - Erwan Bezard
- Univ. Bordeaux, CNRS, IMN, UMR 5293, F-33000 Bordeaux, France; Motac Neuroscience Ltd, Manchester, United Kingdom.
| |
Collapse
|
10
|
Aqueous Self-assembly of Extracted Cyclotides from Viola odorata into Novel Stable Supramolecular Structures. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
11
|
Brunori M, Gianni S. An Outlook on the Complexity of Protein Morphogenesis in Health and Disease. Front Mol Biosci 2022; 9:909567. [PMID: 35769915 PMCID: PMC9234464 DOI: 10.3389/fmolb.2022.909567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
The study of the mechanisms whereby proteins achieve their native functionally competent conformation has been a key issue in molecular biosciences over the last 6 decades. Nevertheless, there are several debated issues and open problems concerning some aspects of this fundamental problem. By considering the emerging complexity of the so-called “native state,” we attempt hereby to propose a personal account on some of the key topics in the field, ranging from the relationships between misfolding and diseases to the significance of protein disorder. Finally, we briefly describe the recent and exciting advances in predicting protein structures from their amino acid sequence.
Collapse
Affiliation(s)
- Maurizio Brunori
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università, Rome, Italy
- Accademia Nazionale dei Lincei, Rome, Italy
- *Correspondence: Maurizio Brunori,
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università, Rome, Italy
| |
Collapse
|
12
|
Landrieu I, Dupré E, Sinnaeve D, El Hajjar L, Smet-Nocca C. Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools. Front Chem 2022; 10:886382. [PMID: 35646824 PMCID: PMC9133342 DOI: 10.3389/fchem.2022.886382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.
Collapse
Affiliation(s)
- Isabelle Landrieu
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Elian Dupré
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Davy Sinnaeve
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Léa El Hajjar
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| |
Collapse
|
13
|
Dharmaraj GL, Arigo FD, Young KA, Martins R, Mancera RL, Bharadwaj P. Novel Amylin Analogues Reduce Amyloid-β Cross-Seeding Aggregation and Neurotoxicity. J Alzheimers Dis 2022; 87:373-390. [PMID: 35275530 DOI: 10.3233/jad-215339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Type 2 diabetes related human islet amyloid polypeptide (hIAPP) plays a dual role in Alzheimer's disease (AD). hIAPP has neuroprotective effects in AD mouse models whereas, high hIAPP concentrations can promote co-aggregation with amyloid-β (Aβ) to promote neurodegeneration. In fact, both low and high plasma hIAPP concentration has been associated with AD. Therefore, non-aggregating hIAPP analogues have garnered interest as a treatment for AD. The aromatic amino acids F23 and I26 in hIAPP have been identified as the key residues involved in self-aggregation and Aβ cross-seeding. OBJECTIVE Three novel IAPP analogues with single and double alanine mutations (A1 = F23, A2 = I26, and A3 = F23 + I26) were assessed for their ability to aggregate, modulate Aβ oligomer formation, and alter neurotoxicity. METHODS A range of biophysical methods including Thioflavin-T, gel electrophoresis, photo-crosslinking, circular dichroism combined with cell viability assays were utilized to assess protein aggregation and toxicity. RESULTS All IAPP analogues showed significantly less self-aggregation than hIAPP. Co-aggregated Aβ 42-A2 and A3 also showed reduced aggregation compared to Aβ 42-hIAPP mixtures. Self- and co-oligomerized A1, A2, and A3 exhibited random coil conformations with reduced beta sheet content compared to hIAPP and Aβ 42-hIAPP aggregates. A1 was toxic at high concentrations compared to A2 and A3. However, co-aggregated Aβ 42-A1, A2, or A3 showed reduced neurotoxicity compared to Aβ 42, hIAPP, and Aβ 42-hIAPP aggregates. CONCLUSION These findings confirm that hIAPP analogues with non-aromatic residues at positions 23 and 26 have reduced self-aggregation and the ability to neutralize Aβ 42 toxicity. This warrants further characterization of their protective effects in pre-clinical AD models.
Collapse
Affiliation(s)
| | - Fraulein Denise Arigo
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
| | - Kimberly A Young
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
| | - Ralph Martins
- Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Perth WA, Australia.,School of Biomedical Science, Macquarie University, Sydney, NSW, Australia
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
| | - Prashant Bharadwaj
- Centre of Excellence for Alzheimer's Disease Research and Care, School of Medical and Health Sciences, Edith Cowan University, Perth WA, Australia.,Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Perth WA, Australia
| |
Collapse
|
14
|
Bezard E, Dehay B. [Aggregation and spread of synuclein in Parkinson's disease]. Med Sci (Paris) 2022; 38:45-51. [PMID: 35060886 DOI: 10.1051/medsci/2021241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The vast majority of neurodegenerative diseases are associated with an accumulation of undegraded and aggregated proteins. Hence the word proteinopathies is now used to refer to these neurodegenerative diseases. The synucleinopathies are one component of them, in particular in Parkinson's disease. The neuropathological features of Parkinson's disease are the progressive loss of dopamine neurons in the midbrain and the formation of aggregates composed mainly of a-synuclein protein. Experimental evidence suggests that under pathological conditions, normal soluble a-synuclein protein adopts an abnormal folding and subsequently aggregates, with a propensity to spread throughout the central nervous system. This review article discusses the specifics of a-synuclein aggregation and emerging mechanisms for understanding its spread and aims at providing a molecular explanation for the progression of the disease in humans.
Collapse
Affiliation(s)
- Erwan Bezard
- Univ. Bordeaux, CNRS, IMN (Institut des maladies neurodégénératives), UMR 5293, 33000 Bordeaux, France
| | - Benjamin Dehay
- Univ. Bordeaux, CNRS, IMN (Institut des maladies neurodégénératives), UMR 5293, 33000 Bordeaux, France
| |
Collapse
|
15
|
Unzipping the Secrets of Amyloid Disassembly by the Human Disaggregase. Cells 2021; 10:cells10102745. [PMID: 34685723 PMCID: PMC8534776 DOI: 10.3390/cells10102745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 01/08/2023] Open
Abstract
Neurodegenerative diseases (NDs) are increasingly positioned as leading causes of global deaths. The accelerated aging of the population and its strong relationship with neurodegeneration forecast these pathologies as a huge global health problem in the upcoming years. In this scenario, there is an urgent need for understanding the basic molecular mechanisms associated with such diseases. A major molecular hallmark of most NDs is the accumulation of insoluble and toxic protein aggregates, known as amyloids, in extracellular or intracellular deposits. Here, we review the current knowledge on how molecular chaperones, and more specifically a ternary protein complex referred to as the human disaggregase, deals with amyloids. This machinery, composed of the constitutive Hsp70 (Hsc70), the class B J-protein DnaJB1 and the nucleotide exchange factor Apg2 (Hsp110), disassembles amyloids of α-synuclein implicated in Parkinson’s disease as well as of other disease-associated proteins such as tau and huntingtin. We highlight recent studies that have led to the dissection of the mechanism used by this chaperone system to perform its disaggregase activity. We also discuss whether this chaperone-mediated disassembly mechanism could be used to solubilize other amyloidogenic substrates. Finally, we evaluate the implications of the chaperone system in amyloid clearance and associated toxicity, which could be critical for the development of new therapies.
Collapse
|
16
|
Roterman I, Stapor K, Fabian P, Konieczny L. In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model. Int J Mol Sci 2021; 22:10587. [PMID: 34638925 PMCID: PMC8508659 DOI: 10.3390/ijms221910587] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 11/17/2022] Open
Abstract
The role of the environment in amyloid formation based on the fuzzy oil drop model (FOD) is discussed here. This model assumes that the hydrophobicity distribution within a globular protein is consistent with a 3D Gaussian (3DG) distribution. Such a distribution is interpreted as the idealized effect of the presence of a polar solvent-water. A chain with a sequence of amino acids (which are bipolar molecules) determined by evolution recreates a micelle-like structure with varying accuracy. The membrane, which is a specific environment with opposite characteristics to the polar aquatic environment, directs the hydrophobic residues towards the surface. The modification of the FOD model to the FOD-M form takes into account the specificity of the cell membrane. It consists in "inverting" the 3DG distribution (complementing the Gaussian distribution), which expresses the exposure of hydrophobic residues on the surface. It turns out that the influence of the environment for any protein (soluble or membrane-anchored) is the result of a consensus factor expressing the participation of the polar environment and the "inverted" environment. The ratio between the proportion of the aqueous and the "reversed" environment turns out to be a characteristic property of a given protein, including amyloid protein in particular. The structure of amyloid proteins has been characterized in the context of prion, intrinsically disordered, and other non-complexing proteins to cover a wider spectrum of molecules with the given characteristics based on the FOD-M model.
Collapse
Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Medyczna 7, 30-688 Kraków, Poland
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Kraków, Poland;
| |
Collapse
|
17
|
Duran-Meza E, Diaz-Espinoza R. Catalytic Amyloids as Novel Synthetic Hydrolases. Int J Mol Sci 2021; 22:ijms22179166. [PMID: 34502074 PMCID: PMC8431744 DOI: 10.3390/ijms22179166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 11/23/2022] Open
Abstract
Amyloids are supramolecular assemblies composed of polypeptides stabilized by an intermolecular beta-sheet core. These misfolded conformations have been traditionally associated with pathological conditions such as Alzheimer’s and Parkinson´s diseases. However, this classical paradigm has changed in the last decade since the discovery that the amyloid state represents a universal alternative fold accessible to virtually any polypeptide chain. Moreover, recent findings have demonstrated that the amyloid fold can serve as catalytic scaffolds, creating new opportunities for the design of novel active bionanomaterials. Here, we review the latest advances in this area, with particular emphasis on the design and development of catalytic amyloids that exhibit hydrolytic activities. To date, three different types of activities have been demonstrated: esterase, phosphoesterase and di-phosphohydrolase. These artificial hydrolases emerge upon the self-assembly of small peptides into amyloids, giving rise to catalytically active surfaces. The highly stable nature of the amyloid fold can provide an attractive alternative for the design of future synthetic hydrolases with diverse applications in the industry, such as the in situ decontamination of xenobiotics.
Collapse
Affiliation(s)
- Eva Duran-Meza
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170022, Chile
- Correspondence:
| |
Collapse
|
18
|
Sharma S, Modi P, Sharma G, Deep S. Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition. Biophys Chem 2021; 278:106665. [PMID: 34419715 DOI: 10.1016/j.bpc.2021.106665] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.
Collapse
Affiliation(s)
- Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Priya Modi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gargi Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| |
Collapse
|
19
|
Koike H, Iguchi Y, Sahashi K, Katsuno M. Significance of Oligomeric and Fibrillar Species in Amyloidosis: Insights into Pathophysiology and Treatment. Molecules 2021; 26:molecules26165091. [PMID: 34443678 PMCID: PMC8401015 DOI: 10.3390/molecules26165091] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Amyloidosis is a term referring to a group of various protein-misfolding diseases wherein normally soluble proteins form aggregates as insoluble amyloid fibrils. How, or whether, amyloid fibrils contribute to tissue damage in amyloidosis has been the topic of debate. In vitro studies have demonstrated the appearance of small globular oligomeric species during the incubation of amyloid beta peptide (Aβ). Nerve biopsy specimens from patients with systemic amyloidosis have suggested that globular structures similar to Aβ oligomers were generated from amorphous electron-dense materials and later developed into mature amyloid fibrils. Schwann cells adjacent to amyloid fibrils become atrophic and degenerative, suggesting that the direct tissue damage induced by amyloid fibrils plays an important role in systemic amyloidosis. In contrast, there is increasing evidence that oligomers, rather than amyloid fibrils, are responsible for cell death in neurodegenerative diseases, particularly Alzheimer’s disease. Disease-modifying therapies based on the pathophysiology of amyloidosis have now become available. Aducanumab, a human monoclonal antibody against the aggregated form of Aβ, was recently approved for Alzheimer’s disease, and other monoclonal antibodies, including gantenerumab, solanezumab, and lecanemab, could also be up for approval. As many other agents for amyloidosis will be developed in the future, studies to develop sensitive clinical scales for identifying improvement and markers that can act as surrogates for clinical scales should be conducted.
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Brunori M. From Kuru to Alzheimer: A personal outlook. Protein Sci 2021; 30:1776-1792. [PMID: 34118168 DOI: 10.1002/pro.4145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 01/02/2023]
Abstract
Seventy years ago, we learned from Chris Anfinsen that the stereochemical code necessary to fold a protein is embedded into its amino acid sequence. In water, protein morphogenesis is a spontaneous reversible process leading from an ensemble of disordered structures to the ordered functionally competent protein; conforming to Aristotle's definition of substance, the synolon of matter and form. The overall process of folding is generally consistent with a two state transition between the native and the denatured protein: not only the denatured state is an ensemble of several structures, but also the native protein populates distinct functionally relevant conformational (sub)states. This two-state view should be revised, given that any globular protein can populate a peculiar third state called amyloid, characterized by an overall architecture that at variance with the native state, is by-and-large independent of the primary structure. In a nut shell, we should accept that beside the folded and unfolded states, any protein can populate a third state called amyloid which gained center stage being the hallmark of incurable neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases as well as others. These fatal diseases are characterized by clear-cut clinical differences, yet display some commonalities such as the presence in the brain of amyloid deposits constituted by one misfolded protein specific for each disease. Some aspects of this complex problem are summarized here as an excursus from the prion's fibrils observed in the brain of aborigines who died of Kuru to the amyloid detectable in the cortex of Alzheimer's patients.
Collapse
Affiliation(s)
- Maurizio Brunori
- Accademia Nazionale dei Lincei and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli,", Sapienza Università di Roma, Rome, Italy
| |
Collapse
|
22
|
Khodaparast L, Wu G, Khodaparast L, Schmidt BZ, Rousseau F, Schymkowitz J. Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention. Front Mol Biosci 2021; 8:681855. [PMID: 34150852 PMCID: PMC8206779 DOI: 10.3389/fmolb.2021.681855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cells have evolved a complex molecular network, collectively called the protein homeostasis (proteostasis) network, to produce and maintain proteins in the appropriate conformation, concentration and subcellular localization. Loss of proteostasis leads to a reduction in cell viability, which occurs to some degree during healthy ageing, but is also the root cause of a group of diverse human pathologies. The accumulation of proteins in aberrant conformations and their aggregation into specific beta-rich assemblies are particularly detrimental to cell viability and challenging to the protein homeostasis network. This is especially true for bacteria; it can be argued that the need to adapt to their changing environments and their high protein turnover rates render bacteria particularly vulnerable to the disruption of protein homeostasis in general, as well as protein misfolding and aggregation. Targeting bacterial proteostasis could therefore be an attractive strategy for the development of novel antibacterial therapeutics. This review highlights advances with an antibacterial strategy that is based on deliberately inducing aggregation of target proteins in bacterial cells aiming to induce a lethal collapse of protein homeostasis. The approach exploits the intrinsic aggregation propensity of regions residing in the hydrophobic core regions of the polypeptide sequence of proteins, which are genetically conserved because of their essential role in protein folding and stability. Moreover, the molecules were designed to target multiple proteins, to slow down the build-up of resistance. Although more research is required, results thus far allow the hope that this strategy may one day contribute to the arsenal to combat multidrug-resistant bacterial infections.
Collapse
Affiliation(s)
- Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| |
Collapse
|
23
|
On the Protein Fibrillation Pathway: Oligomer Intermediates Detection Using ATR-FTIR Spectroscopy. Molecules 2021; 26:molecules26040970. [PMID: 33673072 PMCID: PMC7918411 DOI: 10.3390/molecules26040970] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 01/17/2023] Open
Abstract
Oligomeric intermediates on the pathway of amyloid fibrillation are suspected as the main cytotoxins responsible for amyloid-related pathogenicity. As they appear to be a part of the lag phase of amyloid fibrillation when analyzed using standard methods such as Thioflavin T (ThT) fluorescence, a more sensitive method is needed for their detection. Here we apply Fourier transform infrared spectroscopy (FTIR) in attenuated total reflectance (ATR) mode for fast and cheap analysis of destabilized hen-egg-white lysozyme solution and detection of oligomer intermediates of amyloid fibrillation. Standard methods of protein aggregation analysis— Thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), and 8-anilinonaphthalene-1-sulphonic acid (ANS) fluorescence were applied and compared to FTIR spectroscopy data. Results show the great potential of FTIR for both, qualitative and quantitative monitoring of oligomer formation based on the secondary structure changes. While oligomer intermediates do not induce significant changes in ThT fluorescence, their secondary structure changes were very prominent. Normalization of specific Amide I region peak intensities by using Amide II peak intensity as an internal standard provides an opportunity to use FTIR spectroscopy for both qualitative and quantitative analysis of biological samples and detection of potentially toxic oligomers, as well as for screening of efficiency of fibrillation procedures.
Collapse
|
24
|
Hentschel L, Hansen J, Egelhaaf SU, Platten F. The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson–Boltzmann model of tetragonal lysozyme crystals. Phys Chem Chem Phys 2021; 23:2686-2696. [DOI: 10.1039/d0cp06113a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microcalorimetric and van't Hoff determinations as well as a theoretical description provide a consistent picture of the crystallization enthalpy and entropy of protein solutions and their dependence on physicochemical solution parameters.
Collapse
Affiliation(s)
- Lorena Hentschel
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Jan Hansen
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
| | - Florian Platten
- Condensed Matter Physics Laboratory
- Heinrich Heine University
- 40225 Düsseldorf
- Germany
- Institute of Biological Information Processing (IBI-4: Biomacromolecular Systems and Processes)
| |
Collapse
|
25
|
Jovcevski B, Das S, Smid S, Pukala TL. Polyphenol Honokiol and Flavone 2',3',4'-Trihydroxyflavone Differentially Interact with α-Synuclein at Distinct Phases of Aggregation. ACS Chem Neurosci 2020; 11:4469-4477. [PMID: 33185419 DOI: 10.1021/acschemneuro.0c00654] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The association between protein aggregation and neurodegenerative diseases such as Parkinson's disease continues to be well interrogated but poorly elucidated at a mechanistic level. Nevertheless, the formation of amyloid fibrils from the destabilization and misfolding of native proteins is a molecular hallmark of disease. Consequently, there is ongoing demand for the identification and development of small molecules which prevent fibril formation. This study comprehensively assesses the inhibitory properties of two small molecules, the lignan polyphenol honokiol and the flavonoid 2',3',4'-trihydroxyflavone, in preventing α-synuclein fibrilization. The data shows that honokiol does not prevent α-synuclein fibril elongation, while 2',3',4'-trihydroxyflavone is effective at inhibiting fibril elongation and induces oligomer formation (for both wild-type α-synuclein and the disease-associated A53T mutation). Moreover, the exposed hydrophobicity of α-synuclein fibrils is reduced in the presence of 2',3',4'-trihydroxyflavone, whereas the addition of honokiol did not reduce the hydrophobicity of fibrils. In addition, ion mobility-mass spectrometry revealed that the conformation of α-synuclein wild-type and A53T monomers after disassembly is restored to a nonaggregation-prone state upon 2',3',4'-trihydroxyflavone treatment. Collectively, this study shows that the mechanisms by which these polyphenols and flavonoids prevent fibril formation are distinct by their interactions at various phases of the fibril-forming pathway. Furthermore, this study highlights how thorough biophysical interrogation of the interaction is required for understanding the ability of inhibitors to prevent protein aggregation associated with disease.
Collapse
Affiliation(s)
- Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia, Australia 5005
- Department of Food Science, School of Agriculture, Food & Wine, University of Adelaide, Adelaide, South Australia, Australia 5005
- Adelaide Proteomics Centre, University of Adelaide, Adelaide, South Australia, Australia 5005
| | - Sukanya Das
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, Australia 6102
| | - Scott Smid
- Discipline of Pharmacology, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia 5005
| | - Tara Louise Pukala
- Department of Chemistry, School of Physical Sciences, University of Adelaide, Adelaide, South Australia, Australia 5005
- Adelaide Proteomics Centre, University of Adelaide, Adelaide, South Australia, Australia 5005
| |
Collapse
|
26
|
Polovyi IO, Gnatyuk OP, Pyrshev KO, Hanulia TO, Doroshenko TP, Karakhim SA, Posudievsky OY, Kondratyuk AS, Koshechko VG, Dovbeshko GI. Dual effect of 2D WS 2 nanoparticles on the lysozyme conformation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140556. [PMID: 33075478 DOI: 10.1016/j.bbapap.2020.140556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/17/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
In the present work we studied the effect of 2D WS2 nanoparticles on the conformational changes in lysozyme protein at different pH values (2.0-11.5). The contributions of various structural conformations (α-helix, β-sheets parallel and antiparallel, unordered structure and side groups) were determined by decomposition of Amid I absorbance bands. The 2D WS2 were shown to have different impact on secondary structure depending on pH of the solution and protein concentration. The amyloid fibril presence was confirmed with confocal microscopy enhanced by gold support, and fluorescent spectroscopy with amyloid-sensitive dye Thioflavin T. Our data show that WS2 can both inhibit and stimulate amyloid formation. Additionally, we have also reported an unusual spectroscopic behavior displayed by lysozyme, indicated by narrowing of Amide I and Amide II bands at pH 2.5 and 3.5 when incubated with 2D WS2 nanoparticles.
Collapse
Affiliation(s)
- I O Polovyi
- Institute of Physics of the National Academy of Sciences of Ukraine, Nauky avenue, 46, Kyiv 03028, Ukraine.
| | - O P Gnatyuk
- Institute of Physics of the National Academy of Sciences of Ukraine, Nauky avenue, 46, Kyiv 03028, Ukraine
| | - K O Pyrshev
- Institute of Physics of the National Academy of Sciences of Ukraine, Nauky avenue, 46, Kyiv 03028, Ukraine; O.V. Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, Leontovycha street, 9, Kyiv 01054, Ukraine
| | - T O Hanulia
- Institute of Physics of the National Academy of Sciences of Ukraine, Nauky avenue, 46, Kyiv 03028, Ukraine; Institute of Low Temperature and Structure Research of the Polish Academy of Sciences, Okolna street, 2, Wroclaw 50-422, Poland
| | - T P Doroshenko
- V. Lashkaryov Institute of Semiconductor Physics of the National Academy of Sciences of Ukraine, Nauky avenue, 41, Kyiv 03028, Ukraine
| | - S A Karakhim
- O.V. Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, Leontovycha street, 9, Kyiv 01054, Ukraine
| | - O Yu Posudievsky
- L.V. Pisarzhevsky Institute of Physical Chemistry of the National Academy of Sciences of Ukraine, Nauky avenue, 31, Kyiv 03028, Ukraine
| | - A S Kondratyuk
- L.V. Pisarzhevsky Institute of Physical Chemistry of the National Academy of Sciences of Ukraine, Nauky avenue, 31, Kyiv 03028, Ukraine
| | - V G Koshechko
- L.V. Pisarzhevsky Institute of Physical Chemistry of the National Academy of Sciences of Ukraine, Nauky avenue, 31, Kyiv 03028, Ukraine
| | - G I Dovbeshko
- Institute of Physics of the National Academy of Sciences of Ukraine, Nauky avenue, 46, Kyiv 03028, Ukraine
| |
Collapse
|
27
|
Understanding Mesangial Pathobiology in AL-Amyloidosis and Monoclonal Ig Light Chain Deposition Disease. Kidney Int Rep 2020; 5:1870-1893. [PMID: 33163710 PMCID: PMC7609979 DOI: 10.1016/j.ekir.2020.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
Patients with plasma cell dyscrasias produce free abnormal monoclonal Ig light chains that circulate in the blood stream. Some of them, termed glomerulopathic light chains, interact with the mesangial cells and trigger, in a manner dependent of their structural and physicochemical properties, a sequence of pathological events that results in either light chain–derived (AL) amyloidosis (AL-Am) or light chain deposition disease (LCDD). The mesangial cells play a key role in the pathogenesis of both diseases. The interaction with the pathogenic light chain elicits specific cellular processes, which include apoptosis, phenotype transformation, and secretion of extracellular matrix components and metalloproteinases. Monoclonal light chains associated with AL-Am but not those producing LCDD are avidly endocytosed by mesangial cells and delivered to the mature lysosomal compartment where amyloid fibrils are formed. Light chains from patients with LCDD exert their pathogenic signaling effect at the cell surface of mesangial cells. These events are generic mesangial responses to a variety of adverse stimuli, and they are similar to those characterizing other more frequent glomerulopathies responsible for many cases of end-stage renal disease. The pathophysiologic events that have been elucidated allow to propose future therapeutic approaches aimed at preventing, stopping, ameliorating, or reversing the adverse effects resulting from the interactions between glomerulopathic light chains and mesangium.
Collapse
|
28
|
Milošević J, Petrić J, Jovčić B, Janković B, Polović N. Exploring the potential of infrared spectroscopy in qualitative and quantitative monitoring of ovalbumin amyloid fibrillation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117882. [PMID: 31818644 DOI: 10.1016/j.saa.2019.117882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Amyloid fibrils are highly ordered self-assembled (poly)peptide aggregates with cross-β structural pattern. Ovalbumin was used as a model for exploring the potential of infrared spectroscopy in detecting structural transitions and quantitative monitoring of amyloid fibrillation. Low pH (pH 2) and high temperature (90 °C) over the course of 24 h were conditions applied for amyloid formation. Fibrillation of ovalbumin was monitored by ThT and ANS fluorescence, and SDS PAGE. A significant increase in ThT fluorescence with a plateau reached after 4 h of incubation, without the lag phase, was detected. Structural transitions leading to amyloid fibrillation were analysed using all three Amide regions in ATR-FTIR spectra. Significant changes were detected in Amide I and Amide III region (decrease of α-helix and increase of β-sheet peaks). To establish a fast, precise and simple method for quantitative monitoring of amyloid fibrillation, the Amide I/Amide II ratios of aggregation specific β-sheets (1625 and 1695 cm-1, respectively) with 1540 cm-1 as internal standard were used, resulting in good correlation (R2 = 0.93 and 0.95) with the data observed by monitoring ThT fluorescence. On the other hand, assessing aggregation specific β-sheet contents by self-deconvolution showed lower correlation with ThT fluorescence (R2 = 0.75 and 0.64). Here we examined structural transitions during ovalbumin fibrillation in a qualitative and quantitative manner by exploiting the full potential of Amide regions simultaneously. Secondary structure distribution was monitored using second derivative spectra in Amide I region. A novel, simple mathematical calculation for quantitative monitoring of fibrils formation was presented employing that the increase in low and high frequency aggregation specific β-sheet in Amide I region compared to the internal standard in Amide II region is suitable for fibril formation monitoring.
Collapse
Affiliation(s)
- Jelica Milošević
- University of Belgrade - Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia
| | - Jovan Petrić
- University of Belgrade - Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia
| | - Branko Jovčić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia; Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Brankica Janković
- University of Belgrade - Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia
| | - Natalija Polović
- University of Belgrade - Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia.
| |
Collapse
|
29
|
L. Almeida Z, M. M. Brito R. Structure and Aggregation Mechanisms in Amyloids. Molecules 2020; 25:molecules25051195. [PMID: 32155822 PMCID: PMC7179426 DOI: 10.3390/molecules25051195] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022] Open
Abstract
The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.
Collapse
|
30
|
Chai AB, Leung GKF, Callaghan R, Gelissen IC. P‐glycoprotein: a role in the export of amyloid‐β in Alzheimer's disease? FEBS J 2019; 287:612-625. [DOI: 10.1111/febs.15148] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/09/2019] [Accepted: 11/19/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Amanda B. Chai
- School of Pharmacy Faculty of Medicine and Health University of Sydney Australia
| | - Gavin K. F. Leung
- School of Pharmacy Faculty of Medicine and Health University of Sydney Australia
| | - Richard Callaghan
- Research School of Biology and Medical School Australian National University Canberra Australia
| | - Ingrid C. Gelissen
- School of Pharmacy Faculty of Medicine and Health University of Sydney Australia
| |
Collapse
|
31
|
Chen YT, Hu KW, Huang BJ, Lai CH, Tu LH. Inhibiting Human Calcitonin Fibril Formation with Its Most Relevant Aggregation-Resistant Analog. J Phys Chem B 2019; 123:10171-10180. [PMID: 31692350 DOI: 10.1021/acs.jpcb.9b08514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The most common obstacles to the development of therapeutic polypeptides are peptide stability and aggregation. Human calcitonin (hCT) is a 32-residue hormone polypeptide secreted from the C-cells of the thyroid gland and is responsible for calcium and phosphate regulation in the blood. hCT reduces calcium levels by inhibiting the activity of osteoclasts, which are bone cells that are mainly responsible for breaking down the bone tissue or decreasing the resorption of calcium from the kidneys. Thus, calcitonin injection has been used to treat osteoporosis and Paget's disease of bone. hCT is an aggregation-prone peptide with a high tendency to form amyloid fibrils. As a result, salmon calcitonin (sCT), which is different from hCT at 16-residue positions and has a lower propensity to aggregate, has been chosen as a clinical substitute for hCT. However, significant side effects, including immune reactions, have been shown with the use of sCT injection. In this study, we found that two residues, Tyr-12 and Asn-17, play key roles in inducing the fibrillization of hCT. Double mutation of hCT at these two crucial sites could greatly enhance its resistance to aggregation and provide a peptide-based inhibitor to prevent amyloid formation by hCT. Double-mutated hCT retains its ability to interact with its receptor in vivo. These findings suggest that this variant of hCT would serve as a valuable therapeutic alternative to sCT.
Collapse
Affiliation(s)
- Yi-Ting Chen
- Department of Chemistry , National Taiwan Normal University , Taipei 116 , Taiwan
| | - Kai-Wei Hu
- Department of Chemistry , National Taiwan Normal University , Taipei 116 , Taiwan
| | - Bo-Jie Huang
- Graduate Institute of Biomedical Engineering , National Chung Hsing University , Taichung 402 , Taiwan
| | - Chian-Hui Lai
- Graduate Institute of Biomedical Engineering , National Chung Hsing University , Taichung 402 , Taiwan
| | - Ling-Hsien Tu
- Department of Chemistry , National Taiwan Normal University , Taipei 116 , Taiwan
| |
Collapse
|
32
|
The growth of amyloid fibrils: rates and mechanisms. Biochem J 2019; 476:2677-2703. [DOI: 10.1042/bcj20160868] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022]
Abstract
AbstractAmyloid fibrils are β-sheet-rich linear protein polymers that can be formed by a large variety of different proteins. These assemblies have received much interest in recent decades, due to their role in a range of human disorders. However, amyloid fibrils are also found in a functional context, whereby their structural, mechanical and thermodynamic properties are exploited by biological systems. Amyloid fibrils form through a nucleated polymerisation mechanism with secondary processes acting in many cases to amplify the number of fibrils. The filamentous nature of amyloid fibrils implies that the fibril growth rate is, by several orders of magnitude, the fastest step of the overall aggregation reaction. This article focusses specifically on in vitro experimental studies of the process of amyloid fibril growth, or elongation, and summarises the state of knowledge of its kinetics and mechanisms. This work attempts to provide the most comprehensive summary, to date, of the available experimental data on amyloid fibril elongation rate constants and the temperature and concentration dependence of amyloid fibril elongation rates. These data are compared with those from other types of protein polymers. This comparison with data from other polymerising proteins is interesting and relevant because many of the basic ideas and concepts discussed here were first introduced for non-amyloid protein polymers, most notably by the Japanese school of Oosawa and co-workers for cytoskeletal filaments.
Collapse
|
33
|
Agerschou ED, Flagmeier P, Saridaki T, Galvagnion C, Komnig D, Heid L, Prasad V, Shaykhalishahi H, Willbold D, Dobson CM, Voigt A, Falkenburger B, Hoyer W, Buell AK. An engineered monomer binding-protein for α-synuclein efficiently inhibits the proliferation of amyloid fibrils. eLife 2019; 8:46112. [PMID: 31389332 PMCID: PMC6721797 DOI: 10.7554/elife.46112] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/04/2019] [Indexed: 12/14/2022] Open
Abstract
Removing or preventing the formation of α-synuclein aggregates is a plausible strategy against Parkinson’s disease. To this end, we have engineered the β-wrapin AS69 to bind monomeric α-synuclein with high affinity. In cultured cells, AS69 reduced the self-interaction of α-synuclein and formation of visible α-synuclein aggregates. In flies, AS69 reduced α-synuclein aggregates and the locomotor deficit resulting from α-synuclein expression in neuronal cells. In biophysical experiments in vitro, AS69 highly sub-stoichiometrically inhibited both primary and autocatalytic secondary nucleation processes, even in the presence of a large excess of monomer. We present evidence that the AS69-α-synuclein complex, rather than the free AS69, is the inhibitory species responsible for sub-stoichiometric inhibition of secondary nucleation. These results represent a new paradigm that high affinity monomer binders can lead to strongly sub-stoichiometric inhibition of nucleation processes.
Collapse
Affiliation(s)
| | - Patrick Flagmeier
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | | | - Céline Galvagnion
- RG Mechanisms of Neuroprotection, German Centre for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Pharmacology and Drug Design, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Komnig
- Department of Neurology, RWTH Aachen University, Aachen, Germany
| | - Laetitia Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vibha Prasad
- Department of Neurology, RWTH Aachen University, Aachen, Germany
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Aaron Voigt
- Department of Neurology, RWTH Aachen University, Aachen, Germany
| | - Bjoern Falkenburger
- Department of Neurology, RWTH Aachen University, Aachen, Germany.,Department of Neurology, Dresden University Medical Center, Dresden, Germany.,JARA BRAIN Institute II, Julich and Aachen, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Alexander K Buell
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
34
|
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
| |
Collapse
|
35
|
|
36
|
Williams JK, Yang X, Baum J. Interactions between the Intrinsically Disordered Proteins β-Synuclein and α-Synuclein. Proteomics 2018; 18:e1800109. [PMID: 30142698 PMCID: PMC6447293 DOI: 10.1002/pmic.201800109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/18/2018] [Indexed: 12/31/2022]
Abstract
Several intrinsically disordered proteins have been implicated in the process of amyloid fibril formation in neurodegenerative disease, and developing approaches to inhibit the aggregation of these intrinsically disordered proteins is critical for establishing effective therapies against disease progression. The aggregation pathway of the intrinsically disordered protein alpha-synuclein, which is implicated in several neurodegenerative diseases known as synucleinopathies, has been extensively characterized. Less attention has been leveraged on beta-synuclein, a homologous intrinsically disordered protein that co-localizes with alpha-synuclein and is known to delay alpha-synuclein fibril formation. In this review, we focus on beta-synuclein and the molecular-level interactions between alpha-synuclein and beta-synuclein that underlie the delay of fibril formation. We highlight studies that begin to define alpha-synuclein and beta-synuclein interactions at the monomer, oligomer, and surface levels, and suggest that beta-synuclein plays a role in regulation of inhibition at many different stages of alpha-synuclein aggregation.
Collapse
Affiliation(s)
- Jonathan K Williams
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
| | - Xue Yang
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
| | - Jean Baum
- Department of Chemistry and Chemical Biology, Rutgers University, 08854, Piscataway, New Jersey, USA
| |
Collapse
|
37
|
Kell DB, Pretorius E. No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases. Biol Rev Camb Philos Soc 2018; 93:1518-1557. [PMID: 29575574 PMCID: PMC6055827 DOI: 10.1111/brv.12407] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/12/2018] [Accepted: 02/15/2018] [Indexed: 12/11/2022]
Abstract
Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.
Collapse
Affiliation(s)
- Douglas B. Kell
- School of ChemistryThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- The Manchester Institute of BiotechnologyThe University of Manchester, 131 Princess StreetManchesterLancsM1 7DNU.K.
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
| | - Etheresia Pretorius
- Department of Physiological SciencesStellenbosch University, Stellenbosch Private Bag X1Matieland7602South Africa
| |
Collapse
|
38
|
Illes-Toth E, Rempel DL, Gross ML. Pulsed Hydrogen-Deuterium Exchange Illuminates the Aggregation Kinetics of α-Synuclein, the Causative Agent for Parkinson's Disease. ACS Chem Neurosci 2018; 9:1469-1476. [PMID: 29601177 DOI: 10.1021/acschemneuro.8b00052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
α-Synuclein (aS) forms toxic intermediates ranging from small oligomers and protofibrils to large amyloid fibrils. Understanding the time course of aS fibril formation and the role played by its regions is critical for therapeutic intervention. Here, we used pulsed hydrogen-deuterium exchange and mass spectrometry (HDX-MS) for the first time to probe kinetic intermediates of the full aS aggregation in vitro, achieving kinetic snapshots containing spatially resolved protein information about critical stages. Monitoring the resultant mass shifts shows distinct binomial abundances for two main exchange profiles: one that represents a fast-exchanging, solvent-accessible species and another with a more protected nature. We show using a series of proteolytic peptides from the full protein that self-association is most pronounced in the non-amyloid-β-component region and less so for either terminus. The N-terminus, however, shows a minor protected population at mid- and late times, whereas the C-terminus shows predominantly unimodal HDX, indicating that these regions are devoid of any large conformational rearrangements. Focusing on the hydrophobic core, we confirmed and modeled the different isotopic distributions and calculated their relative fractions to discern their individual contributions. The data fitting reports respective t1/2 values, which are nearly identical and do not depend on location. We followed the aggregation by complementary transmission electron microscopy to observe the morphology of aggregates and circular dichroism to assess changes in secondary structure. Our results provide a detailed picture of aS aggregation in vitro and demonstrate that HDX-MS offers unique spatially resolved, coexisting kinetic intermediates in solution. This new platform is suitable for testing promising inhibitors of aS aggregation.
Collapse
Affiliation(s)
- Eva Illes-Toth
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Don L. Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
39
|
Ruggeri FS, Habchi J, Cerreta A, Dietler G. AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species. Curr Pharm Des 2017; 22:3950-70. [PMID: 27189600 PMCID: PMC5080865 DOI: 10.2174/1381612822666160518141911] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/17/2016] [Indexed: 01/05/2023]
Abstract
Background A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established. Methods: In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species. Conclusion: The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases.
Collapse
Affiliation(s)
- Francesco Simone Ruggeri
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom.
| | | | | | | |
Collapse
|
40
|
Peng Z, Peralta MDR, Toney MD. Extraordinarily Stable Amyloid Fibrils Engineered from Structurally Defined β-Solenoid Proteins. Biochemistry 2017; 56:6041-6050. [DOI: 10.1021/acs.biochem.7b00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zeyu Peng
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Maria D. R. Peralta
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Michael D. Toney
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
41
|
Zapadka KL, Becher FJ, Gomes Dos Santos AL, Jackson SE. Factors affecting the physical stability (aggregation) of peptide therapeutics. Interface Focus 2017; 7:20170030. [PMID: 29147559 DOI: 10.1098/rsfs.2017.0030] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The number of biological therapeutic agents in the clinic and development pipeline has increased dramatically over the last decade and the number will undoubtedly continue to increase in the coming years. Despite this fact, there are considerable challenges in the development, production and formulation of such biologics particularly with respect to their physical stabilities. There are many cases where self-association to form either amorphous aggregates or highly structured fibrillar species limits their use. Here, we review the numerous factors that influence the physical stability of peptides including both intrinsic and external factors, wherever possible illustrating these with examples that are of therapeutic interest. The effects of sequence, concentration, pH, net charge, excipients, chemical degradation and modification, surfaces and interfaces, and impurities are all discussed. In addition, the effects of physical parameters such as pressure, temperature, agitation and lyophilization are described. We provide an overview of the structures of aggregates formed, as well as our current knowledge of the mechanisms for their formation.
Collapse
Affiliation(s)
| | - Frederik J Becher
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | | | - Sophie E Jackson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| |
Collapse
|
42
|
Dharmadana D, Reynolds NP, Conn CE, Valéry C. Molecular interactions of amyloid nanofibrils with biological aggregation modifiers: implications for cytotoxicity mechanisms and biomaterial design. Interface Focus 2017; 7:20160160. [PMID: 28630679 PMCID: PMC5474041 DOI: 10.1098/rsfs.2016.0160] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Amyloid nanofibrils are ubiquitous biological protein fibrous aggregates, with a wide range of either toxic or beneficial activities that are relevant to human disease and normal biology. Protein amyloid fibrillization occurs via nucleated polymerization, through non-covalent interactions. As such, protein nanofibril formation is based on a complex interplay between kinetic and thermodynamic factors. The process entails metastable oligomeric species and a highly thermodynamically favoured end state. The kinetics, and the reaction pathway itself, can be influenced by third party moieties, either molecules or surfaces. Specifically, in the biological context, different classes of biomolecules are known to act as catalysts, inhibitors or modifiers of the generic protein fibrillization process. The biological aggregation modifiers reviewed here include lipid membranes of varying composition, glycosaminoglycans and metal ions, with a final word on xenobiotic compounds. The corresponding molecular interactions are critically analysed and placed in the context of the mechanisms of cytotoxicity of the amyloids involved in diverse pathologies and the non-toxicity of functional amyloids (at least towards their biological host). Finally, the utilization of this knowledge towards the design of bio-inspired and biocompatible nanomaterials is explored.
Collapse
Affiliation(s)
- Durga Dharmadana
- School of Health and Biomedical Sciences, Discipline of Pharmaceutical Sciences, RMIT University, Bundoora, Melbourne, Victoria 3083, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3001, Australia
| | - Nicholas P. Reynolds
- ARC Training Centre for Biodevices, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Charlotte E. Conn
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, Victoria 3001, Australia
| | - Céline Valéry
- School of Health and Biomedical Sciences, Discipline of Pharmaceutical Sciences, RMIT University, Bundoora, Melbourne, Victoria 3083, Australia
| |
Collapse
|
43
|
Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation. Biophys J 2017; 112:868-880. [PMID: 28297646 DOI: 10.1016/j.bpj.2017.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 01/12/2017] [Accepted: 01/17/2017] [Indexed: 11/23/2022] Open
Abstract
Amyloid formation is implicated in a number of human diseases, and is thought to proceed via a nucleation-dependent polymerization mechanism. Experimenters often wish to relate changes in amyloid formation kinetics, for example, in response to small molecules to specific mechanistic steps along this pathway. However, fitting kinetic fibril formation data to a complex model including explicit rate constants results in an ill-posed problem with a vast number of potential solutions. The levels of uncertainty remaining in parameters calculated from these models, arising both from experimental noise and high levels of degeneracy or codependency in parameters, is often unclear. Here, we demonstrate that a combination of explicit mathematical models with an approximate Bayesian computation approach can be used to assign the mechanistic effects of modulators on amyloid fibril formation. We show that even when exact rate constants cannot be extracted, parameters derived from these rate constants can be recovered and used to assign mechanistic effects and their relative magnitudes with a great deal of confidence. Furthermore, approximate Bayesian computation provides a robust method for visualizing uncertainty remaining in the model parameters, regardless of its origin. We apply these methods to the problem of heparin-mediated tau polymerization, which displays complex kinetic behavior not amenable to analysis by more traditional methods. Our analysis indicates that the role of heparin cannot be explained by enhancement of nucleation alone, as has been previously proposed. The methods described here are applicable to a wide range of systems, as models can be easily adapted to account for new reactions and reversibility.
Collapse
|
44
|
Trusova VM, Gorbenko GP. Molecular dynamics simulations of lysozyme-lipid systems: probing the early steps of protein aggregation. J Biomol Struct Dyn 2017; 36:2249-2260. [PMID: 28665188 DOI: 10.1080/07391102.2017.1349691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Using the molecular dynamics simulation, the role of lipids in the lysozyme transition into the aggregation-competent conformation has been clarified. Analysis of the changes of lysozyme secondary structure upon its interactions with the model bilayer membranes composed of phosphatidylcholine and its mixtures with phosphatidylglycerol (10, 40, and 80 mol%) within the time interval of 100 ns showed that lipid-bound protein is characterized by the increased content of β-structures. Along with this, the formation of protein-lipid complexes was accompanied by the increase in the gyration radius and the decrease in RMSD of polypeptide chain. The results obtained were interpreted in terms of the partial unfolding of lysozyme molecule on the lipid matrix, with the magnitude of this effect being increased with increasing the fraction of anionic lipids. Based on the results of molecular dynamics simulation, a hypothetical model of the nucleation of lysozyme amyloid fibrils in a membrane environment was suggested.
Collapse
Affiliation(s)
- Valeriya M Trusova
- a Department of Nuclear and Medical Physics , V.N. Karazin Kharkov National University , 4 Svobody Sq., Kharkov 61022 , Ukraine
| | - Galyna P Gorbenko
- a Department of Nuclear and Medical Physics , V.N. Karazin Kharkov National University , 4 Svobody Sq., Kharkov 61022 , Ukraine
| |
Collapse
|
45
|
Sami N, Rahman S, Kumar V, Zaidi S, Islam A, Ali S, Ahmad F, Hassan MI. Protein aggregation, misfolding and consequential human neurodegenerative diseases. Int J Neurosci 2017; 127:1047-1057. [PMID: 28110595 DOI: 10.1080/00207454.2017.1286339] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins are major components of the biological functions in a cell. Biology demands that a protein must fold into its stable three-dimensional structure to become functional. In an unfavorable cellular environment, protein may get misfolded resulting in its aggregation. These conformational disorders are directly related to the tissue damage resulting in cellular dysfunction giving rise to different diseases. This way, several neurodegenerative diseases such as Alzheimer, Parkinson Huntington diseases and amyotrophic lateral sclerosis are caused. Misfolding of the protein is prevented by innate molecular chaperones of different classes. It is envisaged that work on this line is likely to translate the knowledge into the development of possible strategies for early diagnosis and efficient management of such related human diseases. The present review deals with the human neurodegenerative diseases caused due to the protein misfolding highlighting pathomechanisms and therapeutic intervention.
Collapse
Affiliation(s)
- Neha Sami
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Safikur Rahman
- b Department of Medical Biotechnology , Yeungnam University , Gyeongsan , South Korea
| | - Vijay Kumar
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Sobia Zaidi
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Asimul Islam
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Sher Ali
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Faizan Ahmad
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Md Imtaiyaz Hassan
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| |
Collapse
|
46
|
Abstract
Dozens of proteins are known to convert to the aggregated amyloid state. These include fibrils associated with systemic and neurodegenerative diseases and cancer, functional amyloid fibrils in microorganisms and animals, and many denatured proteins. Amyloid fibrils can be much more stable than other protein assemblies. In contrast to globular proteins, a single protein sequence can aggregate into several distinctly different amyloid structures, termed polymorphs, and a given polymorph can reproduce itself by seeding. Amyloid polymorphs may be the molecular basis of prion strains. Whereas the Protein Data Bank contains some 100,000 globular protein and 3,000 membrane protein structures, only a few dozen amyloid protein structures have been determined, and most of these are short segments of full amyloid-forming proteins. Regardless, these amyloid structures illuminate the architecture of the amyloid state, including its stability and its capacity for formation of polymorphs.
Collapse
Affiliation(s)
- David S Eisenberg
- Howard Hughes Medical Institute and Molecular Biology Institute, University of California, Los Angeles, California 90095-1570; ,
| | - Michael R Sawaya
- Howard Hughes Medical Institute and Molecular Biology Institute, University of California, Los Angeles, California 90095-1570; ,
| |
Collapse
|
47
|
Buell AK. The Nucleation of Protein Aggregates - From Crystals to Amyloid Fibrils. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 329:187-226. [DOI: 10.1016/bs.ircmb.2016.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
48
|
Zapadka KL, Becher FJ, Uddin S, Varley PG, Bishop S, Gomes Dos Santos AL, Jackson SE. A pH-Induced Switch in Human Glucagon-like Peptide-1 Aggregation Kinetics. J Am Chem Soc 2016; 138:16259-16265. [PMID: 27998088 DOI: 10.1021/jacs.6b05025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aggregation and amyloid fibril formation of peptides and proteins is a widespread phenomenon. It has serious implications in a range of areas from biotechnological and pharmaceutical applications to medical disorders. The aim of this study was to develop a better understanding of the mechanism of aggregation and amyloid fibrillation of an important pharmaceutical, human glucagon-like peptide-1 (GLP-1). GLP-1 is a 31-residue hormone peptide that plays an important role regulating blood glucose levels, analogues of which are used for treatment of type 2 diabetes. Amyloid fibril formation of GLP-1 was monitored using thioflavin T fluorescence as a function of peptide concentration between pH 7.5 and 8.2. Results from these studies establish that there is a highly unusual pH-induced switch in GLP-1 aggregation kinetics. At pH 8.2, the kinetics are consistent with a nucleation-polymerization mechanism for fibril formation. However, at pH 7.5, highly unusual kinetics are observed, where the lag time increases with increasing peptide concentration. We attribute this result to the formation of off-pathway species together with an initial slow, unimolecular step where monomer converts to a different monomeric form that forms on-pathway oligomers and ultimately fibrils. Estimation of the pKa values of all the ionizable groups in GLP-1 suggest it is the protonation/deprotonation of the N-terminus that is responsible for the switch with pH. In addition, a range of biophysical techniques were used to characterize (1) the start point of the aggregation reaction and (2) the structure and stability of the fibrils formed. These results show that the off-pathway species form under conditions where GLP-1 is most prone to form oligomers.
Collapse
Affiliation(s)
- Karolina L Zapadka
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Frederik J Becher
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Shahid Uddin
- Formulation Sciences, MedImmune Ltd. , Granta Park, Cambridge CB21 6GH, U.K
| | - Paul G Varley
- Formulation Sciences, MedImmune Ltd. , Granta Park, Cambridge CB21 6GH, U.K
| | - Steve Bishop
- Formulation Sciences, MedImmune , One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | | | - Sophie E Jackson
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| |
Collapse
|
49
|
Kashchiev D. Protein Polymerization into Fibrils from the Viewpoint of Nucleation Theory. Biophys J 2016; 109:2126-36. [PMID: 26588571 DOI: 10.1016/j.bpj.2015.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/30/2015] [Accepted: 10/02/2015] [Indexed: 01/08/2023] Open
Abstract
The assembly of various proteins into fibrillar aggregates is an important phenomenon with wide implications ranging from human disease to nanoscience. Using general kinetic results of nucleation theory, we analyze the polymerization of protein into linear or helical fibrils in the framework of the Oosawa-Kasai (OK) model. We show that while within the original OK model of linear polymerization the process does not involve nucleation, within a modified OK model it is nucleation-mediated. Expressions are derived for the size of the fibril nucleus, the work for fibril formation, the nucleation barrier, the equilibrium and stationary fibril size distributions, and the stationary fibril nucleation rate. Under otherwise equal conditions, this rate decreases considerably when the short (subnucleus) fibrils lose monomers much more frequently than the long (supernucleus) fibrils, a feature that should be born in mind when designing a strategy for stymying or stimulating fibril nucleation. The obtained dependence of the nucleation rate on the concentration of monomeric protein is convenient for experimental verification and for use in rate equations accounting for nucleation-mediated fibril formation. The analysis and the results obtained for linear fibrils are fully applicable to helical fibrils whose formation is describable by a simplified OK model.
Collapse
Affiliation(s)
- Dimo Kashchiev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| |
Collapse
|
50
|
Mattsson N, Schott JM, Hardy J, Turner MR, Zetterberg H. Selective vulnerability in neurodegeneration: insights from clinical variants of Alzheimer's disease. J Neurol Neurosurg Psychiatry 2016; 87:1000-4. [PMID: 26746185 DOI: 10.1136/jnnp-2015-311321] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/05/2015] [Indexed: 11/04/2022]
Abstract
Selective vulnerability in the nervous system refers to the fact that subpopulations of neurons in different brain systems may be more or less prone to abnormal function or death in response to specific types of pathological states or injury. The concept has been used extensively as a potential way of explaining differences in degeneration patterns and the clinical presentation of different neurodegenerative diseases. Yet the increasing complexity of molecular histopathology at the cellular level in neurodegenerative disorders frequently appears at odds with phenotyping based on clinically-directed, macroscopic regional brain involvement. While cross-disease comparisons can provide insights into the differential vulnerability of networks and neuronal populations, we focus here on what is known about selective vulnerability-related factors that might explain the differential phenotypic expressions of the same disease-in this case, typical and atypical forms of Alzheimer's disease. Whereas considerable progress has been made in this area, much is yet to be elucidated; further studies comparing different phenotypic variants aimed at identifying both vulnerability and resilience factors may provide valuable insights into disease pathogenesis, and suggest novel targets for therapy.
Collapse
Affiliation(s)
- Niklas Mattsson
- Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden
| | | | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, Oxford University, Oxford, UK
| | - Henrik Zetterberg
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK Clinical Neurochemistry Laboratory, Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal, Sweden
| |
Collapse
|