1
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Rodríguez-López MA, Coll-Marqués JM, Talens-Perales D, Marín-Navarro J, Polaina J, Vázquez-Contreras E. Analysis of Amyloid Fibrillation of Two Family 1 Glycoside Hydrolases. Int J Mol Sci 2024; 25:8536. [PMID: 39126103 PMCID: PMC11313343 DOI: 10.3390/ijms25158536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
The formation and analysis of amyloid fibers by two β-glucosidases, BglA and BglB, belonging to the GH1 enzyme family, are reported. Both proteins have the (β/α)8 TIM-barrel fold, which is characteristic of this family and is also the most common protein structure. BglA is an octamer, whereas BglB is a monomer. Amyloid fibrillation using pH and temperature as perturbing agents was investigated using fluorescence spectroscopy as a preliminary approach and corroborated using wide-field optical microscopy, confocal microscopy, and field-emission scanning electron microscopy. These analyses showed that both enzymes fibrillate at a wide range of acidic and alkaline conditions and at several temperature conditions, particularly at acidic pH (3-4) and at temperatures between 45 and 65 °C. Circular dichroism spectroscopy corroborated the transition from an α-helix to a β-sheet secondary structure of both proteins in conditions where fibrillation was observed. Overall, our results suggest that fibrillation is a rather common phenomenon caused by protein misfolding, driven by a transition from an α-helix to a β-sheet secondary structure, that many proteins can undergo if subjected to conditions that disturb their native conformation.
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Affiliation(s)
- Miguel A. Rodríguez-López
- Postgraduate in Natural Sciences and Engineering, Autonomous Metropolitan University, Cuajimalpa, Mexico City 05348, Mexico;
- Departament of Natural Sciences, Autonomous Metropolitan University, Cuajimalpa, Mexico City 05348, Mexico
| | - José María Coll-Marqués
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain; (J.M.C.-M.); (D.T.-P.)
| | - David Talens-Perales
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain; (J.M.C.-M.); (D.T.-P.)
| | - Julia Marín-Navarro
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain; (J.M.C.-M.); (D.T.-P.)
- Departament of Biochemistry and Molecular Biology, University of Valencia, 46100 Burjassot, Valencia, Spain
| | - Julio Polaina
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), 46980 Paterna, Valencia, Spain; (J.M.C.-M.); (D.T.-P.)
| | - Edgar Vázquez-Contreras
- Departament of Natural Sciences, Autonomous Metropolitan University, Cuajimalpa, Mexico City 05348, Mexico
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2
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Paschold A, Schäffler M, Miao X, Gardon L, Krüger S, Heise H, Röhr MIS, Ott M, Strodel B, Binder WH. Photocontrolled Reversible Amyloid Fibril Formation of Parathyroid Hormone-Derived Peptides. Bioconjug Chem 2024; 35:981-995. [PMID: 38865349 PMCID: PMC11261605 DOI: 10.1021/acs.bioconjchem.4c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024]
Abstract
Peptide fibrillization is crucial in biological processes such as amyloid-related diseases and hormone storage, involving complex transitions between folded, unfolded, and aggregated states. We here employ light to induce reversible transitions between aggregated and nonaggregated states of a peptide, linked to the parathyroid hormone (PTH). The artificial light-switch 3-{[(4-aminomethyl)phenyl]diazenyl}benzoic acid (AMPB) is embedded into a segment of PTH, the peptide PTH25-37, to control aggregation, revealing position-dependent effects. Through in silico design, synthesis, and experimental validation of 11 novel PTH25-37-derived peptides, we predict and confirm the amyloid-forming capabilities of the AMPB-containing peptides. Quantum-chemical studies shed light on the photoswitching mechanism. Solid-state NMR studies suggest that β-strands are aligned parallel in fibrils of PTH25-37, while in one of the AMPB-containing peptides, β-strands are antiparallel. Simulations further highlight the significance of π-π interactions in the latter. This multifaceted approach enabled the identification of a peptide that can undergo repeated phototriggered transitions between fibrillated and defibrillated states, as demonstrated by different spectroscopic techniques. With this strategy, we unlock the potential to manipulate PTH to reversibly switch between active and inactive aggregated states, representing the first observation of a photostimulus-responsive hormone.
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Affiliation(s)
- André Paschold
- Macromolecular
Chemistry, Institute of Chemistry, Faculty of Natural Science II, Martin Luther University Halle Wittenberg, von-Danckelmann-Platz 4, Halle 06120, Germany
| | - Moritz Schäffler
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52425, Germany
| | - Xincheng Miao
- Center
for Nanosystems Chemistry (CNC), Theodor-Boveri Weg, Universität Würzburg, Würzburg 97074, Germany
| | - Luis Gardon
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52425, Germany
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Stephanie Krüger
- Biozentrum,
Martin Luther University Halle-Wittenberg, Weinberweg 22, Halle 06120, Germany
| | - Henrike Heise
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52425, Germany
- Institut
für Physikalische Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Merle I. S. Röhr
- Center
for Nanosystems Chemistry (CNC), Theodor-Boveri Weg, Universität Würzburg, Würzburg 97074, Germany
| | - Maria Ott
- Institute
of Biophysics, Faculty of Natural Science I, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle 06120, Germany
| | - Birgit Strodel
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Institute
of Biological Information Processing, Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52425, Germany
| | - Wolfgang H. Binder
- Macromolecular
Chemistry, Institute of Chemistry, Faculty of Natural Science II, Martin Luther University Halle Wittenberg, von-Danckelmann-Platz 4, Halle 06120, Germany
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3
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González Díaz A, Cataldi R, Mannini B, Vendruscolo M. Preparation and Characterization of Zn(II)-Stabilized Aβ 42 Oligomers. ACS Chem Neurosci 2024; 15:2586-2599. [PMID: 38979921 PMCID: PMC11258685 DOI: 10.1021/acschemneuro.4c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024] Open
Abstract
Aβ oligomers are being investigated as cytotoxic agents in Alzheimer's disease (AD). Because of their transient nature and conformational heterogeneity, the relationship between the structure and activity of these oligomers is still poorly understood. Hence, methods for stabilizing Aβ oligomeric species relevant to AD are needed to uncover the structural determinants of their cytotoxicity. Here, we build on the observation that metal ions and metabolites have been shown to interact with Aβ, influencing its aggregation and stabilizing its oligomeric species. We thus developed a method that uses zinc ions, Zn(II), to stabilize oligomers produced by the 42-residue form of Aβ (Aβ42), which is dysregulated in AD. These Aβ42-Zn(II) oligomers are small in size, spanning the 10-30 nm range, stable at physiological temperature, and with a broad toxic profile in human neuroblastoma cells. These oligomers offer a tool to study the mechanisms of toxicity of Aβ oligomers in cellular and animal AD models.
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Affiliation(s)
- Alicia González Díaz
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Rodrigo Cataldi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Benedetta Mannini
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department
of Experimental and Clinical Biomedical Sciences Mario Serio, University
of Florence, 50134 Florence, Italy
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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4
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Šneiderienė G, Czekalska MA, Xu CK, Jayaram AK, Krainer G, Arter WE, Peter QAE, Castellana-Cruz M, Saar KL, Levin A, Mueller T, Fiedler S, Devenish SRA, Fiegler H, Kumita JR, Knowles TPJ. α-Synuclein Oligomers Displace Monomeric α-Synuclein from Lipid Membranes. ACS NANO 2024; 18:17469-17482. [PMID: 38916260 PMCID: PMC11238581 DOI: 10.1021/acsnano.3c10889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 06/02/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]
Abstract
Parkinson's disease (PD) is an increasingly prevalent and currently incurable neurodegenerative disorder linked to the accumulation of α-synuclein (αS) protein aggregates in the nervous system. While αS binding to membranes in its monomeric state is correlated to its physiological role, αS oligomerization and subsequent aberrant interactions with lipid bilayers have emerged as key steps in PD-associated neurotoxicity. However, little is known of the mechanisms that govern the interactions of oligomeric αS (OαS) with lipid membranes and the factors that modulate such interactions. This is in large part due to experimental challenges underlying studies of OαS-membrane interactions due to their dynamic and transient nature. Here, we address this challenge by using a suite of microfluidics-based assays that enable in-solution quantification of OαS-membrane interactions. We find that OαS bind more strongly to highly curved, rather than flat, lipid membranes. By comparing the membrane-binding properties of OαS and monomeric αS (MαS), we further demonstrate that OαS bind to membranes with up to 150-fold higher affinity than their monomeric counterparts. Moreover, OαS compete with and displace bound MαS from the membrane surface, suggesting that disruption to the functional binding of MαS to membranes may provide an additional toxicity mechanism in PD. These findings present a binding mechanism of oligomers to model membranes, which can potentially be targeted to inhibit the progression of PD.
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Affiliation(s)
- Greta Šneiderienė
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Magdalena A. Czekalska
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Fluidic
Analytics Limited, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom
- Nencki
Institute of Experimental Biology, Polish
Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Catherine K. Xu
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Akhila K. Jayaram
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Cavendish
Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Georg Krainer
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Institute
of Molecular Biosciences (IMB), University
of Graz, Humboldtstraße
50, 8010 Graz, Austria
| | - William E. Arter
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Quentin A. E. Peter
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Marta Castellana-Cruz
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Kadi Liis Saar
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Aviad Levin
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Thomas Mueller
- Fluidic
Analytics Limited, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom
| | - Sebastian Fiedler
- Fluidic
Analytics Limited, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom
| | - Sean R. A. Devenish
- Fluidic
Analytics Limited, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom
| | - Heike Fiegler
- Fluidic
Analytics Limited, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom
| | - Janet R. Kumita
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
- Cavendish
Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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5
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Axell E, Hu J, Lindberg M, Dear AJ, Ortigosa-Pascual L, Andrzejewska EA, Šneiderienė G, Thacker D, Knowles TPJ, Sparr E, Linse S. The role of shear forces in primary and secondary nucleation of amyloid fibrils. Proc Natl Acad Sci U S A 2024; 121:e2322572121. [PMID: 38875148 PMCID: PMC11194593 DOI: 10.1073/pnas.2322572121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/02/2024] [Indexed: 06/16/2024] Open
Abstract
Shear forces affect self-assembly processes ranging from crystallization to fiber formation. Here, the effect of mild agitation on amyloid fibril formation was explored for four peptides and investigated in detail for A[Formula: see text]42, which is associated with Alzheimer's disease. To gain mechanistic insights into the effect of mild agitation, nonseeded and seeded aggregation reactions were set up at various peptide concentrations with and without an inhibitor. First, an effect on fibril fragmentation was excluded by comparing the monomer-concentration dependence of aggregation kinetics under idle and agitated conditions. Second, using a secondary nucleation inhibitor, Brichos, the agitation effect on primary nucleation was decoupled from secondary nucleation. Third, an effect on secondary nucleation was established in the absence of inhibitor. Fourth, an effect on elongation was excluded by comparing the seeding potency of fibrils formed under idle or agitated conditions. We find that both primary and secondary nucleation steps are accelerated by gentle agitation. The increased shear forces facilitate both the detachment of newly formed aggregates from catalytic surfaces and the rate at which molecules are transported in the bulk solution to encounter nucleation sites on the fibril and other surfaces. Ultrastructural evidence obtained with cryogenic transmission electron microscopy and free-flow electrophoresis in microfluidics devices imply that agitation speeds up the detachment of nucleated species from the fibril surface. Our findings shed light on the aggregation mechanism and the role of detachment for efficient secondary nucleation. The results inform on how to modulate the relative importance of different microscopic steps in drug discovery and investigations.
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Affiliation(s)
- Emil Axell
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Jing Hu
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Max Lindberg
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Alexander J. Dear
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Lei Ortigosa-Pascual
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Ewa A. Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Greta Šneiderienė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Dev Thacker
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Cambridge University, CB2 1EWCambridge, United Kingdom
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, SE-221 00Lund, Sweden
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6
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Keith A, Brichtová EP, Barber JG, Wales DJ, Jackson SE, Röder K. Energy Landscapes and Structural Ensembles of Glucagon-like Peptide-1 Monomers. J Phys Chem B 2024; 128:5601-5611. [PMID: 38831581 PMCID: PMC11182347 DOI: 10.1021/acs.jpcb.4c01794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
While GLP-1 and its analogues are important pharmaceutical agents in the treatment of type 2 diabetes and obesity, their susceptibility to aggregate into amyloid fibrils poses a significant safety issue. Many factors may contribute to the aggregation propensity, including pH. While it is known that the monomeric structure of GLP-1 has a strong impact on primary nucleation, probing its diverse structural ensemble is challenging. Here, we investigated the monomer structural ensembles at pH 3, 4, and 7.5 using state-of-the-art computational methods in combination with experimental data. We found significant stabilization of β-strand structures and destabilization of helical structures at lower pH, correlating with observed aggregation lag times, which are lower under these conditions. We further identified helical defects at pH 4, which led to the fastest observed aggregation, in agreement with our far-UV circular dichroism data. The detailed atomistic structures that result from the computational studies help to rationalize the experimental results on the aggregation propensity of GLP-1. This work provides a new insight into the pH-dependence of monomeric structural ensembles of GLP-1 and connects them to experimental observations.
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Affiliation(s)
- Alasdair
D. Keith
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Now:
Department of Biochemistry, School of Medicine, Emory University, 1510 Clifton Rd NE, Atlanta, Georgia 30322, United States
| | - Eva Přáda Brichtová
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Now:
Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorferstr. 1A, Vienna 1060, Austria
| | - Jack G. Barber
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Sophie E. Jackson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Konstantin Röder
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Now:
Randall Centre for Cell & Molecular Biophysics, King’s College London, Great Maze Pond, London SE1 1UL, U.K.
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7
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Wei J, Meisl G, Dear A, Oosterhuis M, Melki R, Emanuelsson C, Linse S, Knowles TPJ. Kinetic models reveal the interplay of protein production and aggregation. Chem Sci 2024; 15:8430-8442. [PMID: 38846392 PMCID: PMC11151821 DOI: 10.1039/d4sc00088a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Protein aggregation is a key process in the development of many neurodegenerative disorders, including dementias such as Alzheimer's disease. Significant progress has been made in understanding the molecular mechanisms of aggregate formation in pure buffer systems, much of which was enabled by the development of integrated rate laws that allowed for mechanistic analysis of aggregation kinetics. However, in order to translate these findings into disease-relevant conclusions and to make predictions about the effect of potential alterations to the aggregation reactions by the addition of putative inhibitors, the current models need to be extended to account for the altered situation encountered in living systems. In particular, in vivo, the total protein concentrations typically do not remain constant and aggregation-prone monomers are constantly being produced but also degraded by cells. Here, we build a theoretical model that explicitly takes into account monomer production, derive integrated rate laws and discuss the resulting scaling laws and limiting behaviours. We demonstrate that our models are suited for the aggregation-prone Huntington's disease-associated peptide HttQ45 utilizing a system for continuous in situ monomer production and the aggregation of the tumour suppressor protein P53. The aggregation-prone HttQ45 monomer was produced through enzymatic cleavage of a larger construct in which a fused protein domain served as an internal inhibitor. For P53, only the unfolded monomers form aggregates, making the unfolding a rate-limiting step which constitutes a source of aggregation-prone monomers. The new model opens up possibilities for a quantitative description of aggregation in living systems, allowing for example the modelling of inhibitors of aggregation in a dynamic environment of continuous protein synthesis.
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Affiliation(s)
- Jiapeng Wei
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Alexander Dear
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Department of Biochemistry and Structural Biology, Lund University SE22100 Lund Sweden
| | - Matthijs Oosterhuis
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS 18 Route du Panorama, Fontenay-Aux-Roses cedex 92265 France
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University Sweden
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University Lund Sweden
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cavendish Laboratory, University of Cambridge J J Thomson Avenue CB3 0HE UK
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8
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Dear A, Thacker D, Wennmalm S, Ortigosa-Pascual L, Andrzejewska EA, Meisl G, Linse S, Knowles TPJ. Aβ Oligomer Dissociation Is Catalyzed by Fibril Surfaces. ACS Chem Neurosci 2024; 15:2296-2307. [PMID: 38785363 PMCID: PMC11157482 DOI: 10.1021/acschemneuro.4c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Oligomeric assemblies consisting of only a few protein subunits are key species in the cytotoxicity of neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. Their lifetime in solution and abundance, governed by the balance of their sources and sinks, are thus important determinants of disease. While significant advances have been made in elucidating the processes that govern oligomer production, the mechanisms behind their dissociation are still poorly understood. Here, we use chemical kinetic modeling to determine the fate of oligomers formed in vitro and discuss the implications for their abundance in vivo. We discover that oligomeric species formed predominantly on fibril surfaces, a broad class which includes the bulk of oligomers formed by the key Alzheimer's disease-associated Aβ peptides, also dissociate overwhelmingly on fibril surfaces, not in solution as had previously been assumed. We monitor this "secondary nucleation in reverse" by measuring the dissociation of Aβ42 oligomers in the presence and absence of fibrils via two distinct experimental methods. Our findings imply that drugs that bind fibril surfaces to inhibit oligomer formation may also inhibit their dissociation, with important implications for rational design of therapeutic strategies for Alzheimer's and other amyloid diseases.
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Affiliation(s)
- Alexander
J. Dear
- Biochemistry
and Structural Biology, Lund University, Lund 221 00, Sweden
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Dev Thacker
- Biochemistry
and Structural Biology, Lund University, Lund 221 00, Sweden
| | - Stefan Wennmalm
- Department
of Applied Physics, Biophysics Group, SciLifeLab, Royal Institute of Technology-KTH, Solna 171 65, Sweden
| | | | - Ewa A. Andrzejewska
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Georg Meisl
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Sara Linse
- Biochemistry
and Structural Biology, Lund University, Lund 221 00, Sweden
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Cavendish
Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, U.K.
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9
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Torricella F, Tugarinov V, Clore GM. Nucleation of Huntingtin Aggregation Proceeds via Conformational Conversion of Pre-Formed, Sparsely-Populated Tetramers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309217. [PMID: 38476051 PMCID: PMC11199967 DOI: 10.1002/advs.202309217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/18/2024] [Indexed: 03/14/2024]
Abstract
Pathogenic huntingtin exon-1 protein (httex1), characterized by an expanded polyglutamine tract located between the N-terminal amphiphilic region and a C-terminal polyproline-rich domain, forms fibrils that accumulate in neuronal inclusion bodies, and is associated with a fatal, autosomal dominant neurodegenerative condition known as Huntington's disease. Here a complete kinetic model is described for aggregation/fibril formation of a httex1 construct with a 35-residue polyglutamine repeat, httex1Q35. Using exchange NMR spectroscopy, it is previously shown that the reversible formation of a sparsely-populated tetramer of the N-terminal amphiphilic domain of httex1Q35, comprising a D2 symmetric four-helix bundle, occurs on the microsecond time-scale and is a prerequisite for subsequent nucleation and fibril formation on a time scale that is many orders of magnitude slower (hours). Here a unified kinetic model of httex1Q35 aggregation is developed in which fast, reversible tetramerization is directly linked to slow irreversible fibril formation via conversion of pre-equilibrated tetrameric species to "active", chain elongation-capable nuclei by conformational re-arrangement with a finite, monomer-independent rate. The unified model permits global quantitative analysis of reversible tetramerization and irreversible fibril formation from a time series of 1H-15N correlation spectra recorded during the course of httex1Q35 aggregation.
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Affiliation(s)
- Francesco Torricella
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD20892‐0520USA
| | - Vitali Tugarinov
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD20892‐0520USA
| | - G. Marius Clore
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaMD20892‐0520USA
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10
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Santos J, Cuellar J, Pallarès I, Byrd EJ, Lends A, Moro F, Abdul-Shukkoor MB, Pujols J, Velasco-Carneros L, Sobott F, Otzen DE, Calabrese AN, Muga A, Pedersen JS, Loquet A, Valpuesta JM, Radford SE, Ventura S. A Targetable N-Terminal Motif Orchestrates α-Synuclein Oligomer-to-Fibril Conversion. J Am Chem Soc 2024; 146:12702-12711. [PMID: 38683963 PMCID: PMC11082882 DOI: 10.1021/jacs.4c02262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Oligomeric species populated during α-synuclein aggregation are considered key drivers of neurodegeneration in Parkinson's disease. However, the development of oligomer-targeting therapeutics is constrained by our limited knowledge of their structure and the molecular determinants driving their conversion to fibrils. Phenol-soluble modulin α3 (PSMα3) is a nanomolar peptide binder of α-synuclein oligomers that inhibits aggregation by blocking oligomer-to-fibril conversion. Here, we investigate the binding of PSMα3 to α-synuclein oligomers to discover the mechanistic basis of this protective activity. We find that PSMα3 selectively targets an α-synuclein N-terminal motif (residues 36-61) that populates a distinct conformation in the mono- and oligomeric states. This α-synuclein region plays a pivotal role in oligomer-to-fibril conversion as its absence renders the central NAC domain insufficient to prompt this structural transition. The hereditary mutation G51D, associated with early onset Parkinson's disease, causes a conformational fluctuation in this region, leading to delayed oligomer-to-fibril conversion and an accumulation of oligomers that are resistant to remodeling by molecular chaperones. Overall, our findings unveil a new targetable region in α-synuclein oligomers, advance our comprehension of oligomer-to-amyloid fibril conversion, and reveal a new facet of α-synuclein pathogenic mutations.
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Affiliation(s)
- Jaime Santos
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Jorge Cuellar
- Department
of Macromolecular Structures, Centro Nacional
de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Irantzu Pallarès
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Emily J. Byrd
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alons Lends
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac 33600, France
| | - Fernando Moro
- Instituto
Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología
Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, Leioa 48940, Spain
| | | | - Jordi Pujols
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Lorea Velasco-Carneros
- Instituto
Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología
Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, Leioa 48940, Spain
| | - Frank Sobott
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Daniel E. Otzen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Molecular Biology and
Genetics, Aarhus University, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Antonio N. Calabrese
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Arturo Muga
- Instituto
Biofisika (UPV/EHU, CSIC) y Dpto. de Bioquímica y Biología
Molecular, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Barrio Sarriena S/N, Leioa 48940, Spain
| | - Jan Skov Pedersen
- Interdisciplinary
Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, Aarhus C 8000, Denmark
| | - Antoine Loquet
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac 33600, France
| | - Jose María Valpuesta
- Department
of Macromolecular Structures, Centro Nacional
de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology, School of Molecular and Cellular
Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Salvador Ventura
- Institut
de Biotecnologia i Biomedicina and Departament de Bioquímica
i Biologia Molecular, Universitat Autònoma
de Barcelona, Bellaterra, Barcelona 08193, Spain
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11
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Espay AJ, Lees AJ. Loss of monomeric alpha-synuclein (synucleinopenia) and the origin of Parkinson's disease. Parkinsonism Relat Disord 2024; 122:106077. [PMID: 38461037 DOI: 10.1016/j.parkreldis.2024.106077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
These facts argue against the gain-of-function synucleinopathy hypothesis, which proposes that Lewy pathology causes Parkinson's disease: (1) most brains from people without neurological symptoms have multiple pathologies; (2) neither pathology type nor distribution correlate with disease severity or progression in Parkinson's disease; (3) aggregated α-synuclein in the form of Lewy bodies is not a space-occupying lesion but the insoluble fraction of its precursor, soluble monomeric α-synuclein; (4) pathology spread is passive, occurring by irreversible nucleation, not active replication; and (5) low cerebrospinal fluid α-synuclein levels predict brain atrophy and clinical disease progression. The transformation of α-synuclein into Lewy pathology may occur as a response to biological, toxic, or infectious stressors whose persistence perpetuates the nucleation process, depleting normal α-synuclein and eventually leading to Parkinson's symptoms from neuronal death. We propose testing the loss-of-function synucleinopenia hypothesis by evaluating the clinical and neurodegenerative rescue effect of replenishing the levels of monomeric α-synuclein.
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Affiliation(s)
- Alberto J Espay
- James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, USA.
| | - Andrew J Lees
- The National Hospital, Queen Square and Reta Lila Weston Institute for Neurological Studies University College London, London, UK
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12
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Santos J, Pallarès I, Ventura S. A glimpse into the structural properties of α-synuclein oligomers. Biofactors 2024; 50:439-449. [PMID: 38063360 DOI: 10.1002/biof.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/03/2023] [Indexed: 06/15/2024]
Abstract
α-Synuclein (αS) aggregation is the main neurological hallmark of a group of debilitating neurodegenerative disorders, collectively referred to as synucleinopathies, of which Parkinson's disease is the most prevalent. αS oligomers formed during the initial stages of aggregation are considered key pathogenic drivers of disease onset and progression, standing as privileged targets for therapeutic intervention and diagnosis. However, the structure of αS oligomers and the mechanistic basis of oligomer to fibril conversion are yet poorly understood, thereby precluding the rational formulation of strategies aimed at targeting oligomeric species. In this review, we delve into the recent advances in the structural and mechanistic characterization of αS oligomers. We also discuss how these advances are transforming our understanding of these elusive species and paving the way for oligomer-targeting therapeutics and diagnosis.
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Affiliation(s)
- Jaime Santos
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irantzu Pallarès
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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13
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Abioye A, Akintade D, Mitchell J, Olorode S, Adejare A. Nonintuitive Immunogenicity and Plasticity of Alpha-Synuclein Conformers: A Paradigm for Smart Delivery of Neuro-Immunotherapeutics. Pharmaceutics 2024; 16:609. [PMID: 38794271 PMCID: PMC11124533 DOI: 10.3390/pharmaceutics16050609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Despite the extensive research successes and continuous developments in modern medicine in terms of diagnosis, prevention, and treatment, the lack of clinically useful disease-modifying drugs or immunotherapeutic agents that can successfully treat or prevent neurodegenerative diseases is an ongoing challenge. To date, only one of the 244 drugs in clinical trials for the treatment of neurodegenerative diseases has been approved in the past decade, indicating a failure rate of 99.6%. In corollary, the approved monoclonal antibody did not demonstrate significant cognitive benefits. Thus, the prevalence of neurodegenerative diseases is increasing rapidly. Therefore, there is an urgent need for creative approaches to identifying and testing biomarkers for better diagnosis, prevention, and disease-modifying strategies for the treatment of neurodegenerative diseases. Overexpression of the endogenous α-synuclein has been identified as the driving force for the formation of the pathogenic α-synuclein (α-Syn) conformers, resulting in neuroinflammation, hypersensitivity, endogenous homeostatic responses, oxidative dysfunction, and degeneration of dopaminergic neurons in Parkinson's disease (PD). However, the conformational plasticity of α-Syn proffers that a certain level of α-Syn is essential for the survival of neurons. Thus, it exerts both neuroprotective and neurotoxic (regulatory) functions on neighboring neuronal cells. Furthermore, the aberrant metastable α-Syn conformers may be subtle and difficult to detect but may trigger cellular and molecular events including immune responses. It is well documented in literature that the misfolded α-Syn and its conformers that are released into the extracellular space from damaged or dead neurons trigger the innate and adaptive immune responses in PD. Thus, in this review, we discuss the nonintuitive plasticity and immunogenicity of the α-Syn conformers in the brain immune cells and their physiological and pathological consequences on the neuroimmune responses including neuroinflammation, homeostatic remodeling, and cell-specific interactions that promote neuroprotection in PD. We also critically reviewed the novel strategies for immunotherapeutic delivery interventions in PD pathogenesis including immunotherapeutic targets and potential nanoparticle-based smart drug delivery systems. It is envisioned that a greater understanding of the nonintuitive immunogenicity of aberrant α-Syn conformers in the brain's microenvironment would provide a platform for identifying valid therapeutic targets and developing smart brain delivery systems for clinically effective disease-modifying immunotherapeutics that can aid in the prevention and treatment of PD in the future.
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Affiliation(s)
- Amos Abioye
- College of Pharmacy and Health Sciences, Belmont University, Nashville, TN 37212, USA
| | - Damilare Akintade
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - James Mitchell
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - Simisade Olorode
- Department of Biomedical Sciences, School of Health, Leeds Beckett University, Leeds LS1 3HE, UK; (D.A.); (J.M.); (S.O.)
| | - Adeboye Adejare
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, Saint Joseph’s University, Philadelphia, PA 19131, USA;
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14
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Meyer N, Torrent J, Balme S. Characterizing Prion-Like Protein Aggregation: Emerging Nanopore-Based Approaches. SMALL METHODS 2024:e2400058. [PMID: 38644684 DOI: 10.1002/smtd.202400058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/10/2024] [Indexed: 04/23/2024]
Abstract
Prion-like protein aggregation is characteristic of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. This process involves the formation of aggregates ranging from small and potentially neurotoxic oligomers to highly structured self-propagating amyloid fibrils. Various approaches are used to study protein aggregation, but they do not always provide continuous information on the polymorphic, transient, and heterogeneous species formed. This review provides an updated state-of-the-art approach to the detection and characterization of a wide range of protein aggregates using nanopore technology. For each type of nanopore, biological, solid-state polymer, and nanopipette, discuss the main achievements for the detection of protein aggregates as well as the significant contributions to the understanding of protein aggregation and diagnostics.
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Affiliation(s)
- Nathan Meyer
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Joan Torrent
- INM, University of Montpellier, INSERM, Montpellier, 34095, France
| | - Sébastien Balme
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, Cedex 5, Montpellier, 34095, France
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15
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Yuzu K, Imamura H, Nozaki T, Fujii Y, Badawy SMM, Morishima K, Okuda A, Inoue R, Sugiyama M, Chatani E. Mechanistic Modeling of Amyloid Oligomer and Protofibril Formation in Bovine Insulin. J Mol Biol 2024; 436:168461. [PMID: 38301805 DOI: 10.1016/j.jmb.2024.168461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Early phase of amyloid formation, where prefibrillar aggregates such as oligomers and protofibrils are often observed, is crucial for understanding pathogenesis. However, the detailed mechanisms of their formation have been difficult to elucidate because they tend to form transiently and heterogeneously. Here, we found that bovine insulin protofibril formation proceeds in a monodisperse manner, which allowed us to characterize the detailed early aggregation process by light scattering in combination with thioflavin T fluorescence and Fourier transform infrared spectroscopy. The protofibril formation was specific to bovine insulin, whereas no significant aggregation was observed in human insulin. The kinetic analysis combining static and dynamic light scattering data revealed that the protofibril formation process in bovine insulin can be divided into two steps based on fractal dimension. When modeling the experimental data based on Smoluchowski aggregation kinetics, an aggregation scheme consisting of initial fractal aggregation forming spherical oligomers and their subsequent end-to-end association forming protofibrils was clarified. Furthermore, the analysis of temperature and salt concentration dependencies showed that the end-to-end association is the rate-limiting step, involving dehydration. The established model for protofibril formation, wherein oligomers are incorporated as a precursor, provides insight into the molecular mechanism by which protein molecules assemble during the early stage of amyloid formation.
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Affiliation(s)
- Keisuke Yuzu
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Imamura
- Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Takuro Nozaki
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Yuki Fujii
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Shaymaa Mohamed Mohamed Badawy
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan; Department of Agricultural Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan.
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16
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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17
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Samdin TD, Jones CR, Guaglianone G, Kreutzer AG, Freites JA, Wierzbicki M, Nowick JS. A β-barrel-like tetramer formed by a β-hairpin derived from Aβ. Chem Sci 2023; 15:285-297. [PMID: 38131075 PMCID: PMC10732006 DOI: 10.1039/d3sc05185d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
β-Hairpins formed by the β-amyloid peptide Aβ are building blocks of Aβ oligomers. Three different alignments of β-hairpins have been observed in the structures of Aβ oligomers or fibrils. Differences in β-hairpin alignment likely contribute to the heterogeneity of Aβ oligomers and thus impede their study at high-resolution. Here, we designed, synthesized, and studied a series of β-hairpin peptides derived from Aβ12-40 in one of these three alignments and investigated their solution-phase assembly and folding. These assays reveal the formation of tetramers and octamers that are stabilized by intermolecular hydrogen bonding interactions between Aβ residues 12-14 and 38-40 as part of an extended β-hairpin conformation. X-ray crystallographic studies of one peptide from this series reveal the formation of β-barrel-like tetramers and octamers that are stabilized by edge-to-edge hydrogen bonding and hydrophobic packing. Dye-leakage and caspase 3/7 activation assays using tetramer and octamer forming peptides from this series reveal membrane-damaging and apoptotic properties. A molecular dynamics simulation of the β-barrel-like tetramer embedded in a lipid bilayer shows membrane disruption and water permeation. The tetramers and octamers described herein provide additional models of how Aβ may assemble into oligomers and supports the hypothesis that β-hairpin alignment and topology may contribute directly to oligomer heterogeneity.
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Affiliation(s)
- Tuan D Samdin
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Chelsea R Jones
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Gretchen Guaglianone
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Adam G Kreutzer
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - J Alfredo Freites
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - Michał Wierzbicki
- Department of Chemistry, University of California Irvine California 92697-2025 USA
| | - James S Nowick
- Department of Chemistry, University of California Irvine California 92697-2025 USA
- Department of Pharmaceutical Sciences, University of California, Irvine Irvine California 92697-2025 USA
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18
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Portugal Barron D, Guo Z. The supersaturation perspective on the amyloid hypothesis. Chem Sci 2023; 15:46-54. [PMID: 38131088 PMCID: PMC10731913 DOI: 10.1039/d3sc03981a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/27/2023] [Indexed: 12/23/2023] Open
Abstract
Development of therapeutic interventions for Alzheimer's over the past three decades has been guided by the amyloid hypothesis, which puts Aβ deposition as the initiating event of a pathogenic cascade leading to dementia. In the current form, the amyloid hypothesis lacks a comprehensive framework that considers the complex nature of Aβ aggregation. The explanation of how Aβ deposition leads to downstream pathology, and how reducing Aβ plaque load via anti-amyloid therapy can lead to improvement in cognition remains insufficient. In this perspective we integrate the concept of Aβ supersaturation into the amyloid hypothesis, laying out a framework for the mechanistic understanding and therapeutic intervention of Alzheimer's disease. We discuss the important distinction between in vitro and in vivo patterns of Aβ aggregation, the impact of different aggregation stages on therapeutic strategies, and how future investigations could integrate this concept in order to produce a more thorough understanding and better treatment for Alzheimer's and other amyloid-related disorders.
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Affiliation(s)
- Diana Portugal Barron
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer's Research and Care, David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer's Research and Care, David Geffen School of Medicine, University of California, Los Angeles Los Angeles CA USA
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19
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Le NTK, Kang EJ, Park JH, Kang K. Catechol-Amyloid Interactions. Chembiochem 2023; 24:e202300628. [PMID: 37850717 DOI: 10.1002/cbic.202300628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/19/2023]
Abstract
This review introduces multifaceted mutual interactions between molecules containing a catechol moiety and aggregation-prone proteins. The complex relationships between these two molecular species have previously been elucidated primarily in a unidirectional manner, as demonstrated in cases involving the development of catechol-based inhibitors for amyloid aggregation and the elucidation of the role of functional amyloid fibers in melanin biosynthesis. This review aims to consolidate scattered clues pertaining to catechol-based amyloid inhibitors, functional amyloid scaffold of melanin biosynthesis, and chemically designed peptide fibers for providing chemical insights into the role of the local three-dimensional orientation of functional groups in manifesting such interactions. These orientations may play crucial, yet undiscovered, roles in various supramolecular structures.
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Affiliation(s)
- Nghia T K Le
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Eun Joo Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Ji Hun Park
- Department of Science Education, Ewha Womans University, Seoul, 03760, South Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
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20
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Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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21
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Sandler S, Horne RI, Rocchetti S, Novak R, Hsu NS, Castellana Cruz M, Faidon Brotzakis Z, Gregory RC, Chia S, Bernardes GJL, Keyser UF, Vendruscolo M. Multiplexed Digital Characterization of Misfolded Protein Oligomers via Solid-State Nanopores. J Am Chem Soc 2023; 145:25776-25788. [PMID: 37972287 PMCID: PMC10690769 DOI: 10.1021/jacs.3c09335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
Misfolded protein oligomers are of central importance in both the diagnosis and treatment of Alzheimer's and Parkinson's diseases. However, accurate high-throughput methods to detect and quantify oligomer populations are still needed. We present here a single-molecule approach for the detection and quantification of oligomeric species. The approach is based on the use of solid-state nanopores and multiplexed DNA barcoding to identify and characterize oligomers from multiple samples. We study α-synuclein oligomers in the presence of several small-molecule inhibitors of α-synuclein aggregation as an illustration of the potential applicability of this method to the development of diagnostic and therapeutic methods for Parkinson's disease.
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Affiliation(s)
- Sarah
E. Sandler
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Robert I. Horne
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Sara Rocchetti
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Robert Novak
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Nai-Shu Hsu
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Marta Castellana Cruz
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Z. Faidon Brotzakis
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Rebecca C. Gregory
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Bioprocessing
Technology Institute, Agency for Science, Technology and Research
(A*STAR), Singapore 138668
| | - Gonçalo J. L. Bernardes
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Ulrich F. Keyser
- Cavendish
Laboratory, Maxwell Centre, Department of Physics, University of Cambridge, Cambridge CB3 0HE, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
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22
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Das BK, Singh O, Chakraborty D. Exploring the Barriers in the Aggregation of a Hexadecameric Human Prion Peptide through the Markov State Model. ACS Chem Neurosci 2023; 14:3622-3645. [PMID: 37705330 DOI: 10.1021/acschemneuro.3c00284] [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: 09/15/2023] Open
Abstract
The prefibrillar aggregation kinetics of prion peptides are still an enigma. In this perspective, we employ atomistic molecular dynamics (MD) simulations of the shortest human prion peptide (HPP) (127GYMLGS132) at various temperatures and peptide concentrations and apply the Markov state model to determine the various intermediates and lag phases. Our results reveal that the natural mechanism of prion peptide self-assembly in the aqueous phase is impeded by two significant kinetic barriers with oligomer sizes of 6-9 and 12-13 peptides, respectively. The first one is the aggregation of unstructured lower-order oligomers, and the second is fibril nucleation, which impedes the further growth of prion aggregates. Among these two activation barriers, the second one is found to be dominant irrespective of the increase in temperature and peptide concentration. These lag phases are captured in all three different force-field parameters, namely, GROMOS-54a7, AMBER-99SB-ILDN, and CHARMMS 36m, at different concentrations. The GROMOS-54a7 and AMBER-99SB-ILDN force fields showed a comparatively higher percentage of β-sheet formation in the metastable aggregate that evolved during the aggregation process. In contrast, the CHARMM-36m force field showed mostly coil or turn conformations. The addition of a novel catecholamine derivative (naphthoquinone dopamine (NQDA)) arrests the aggregation process between the lag phases by increasing the activation barrier for the Lag1 and Lag2 phases in all of the force fields, which further validates the existence of these lag phases. The preferential binding of NQDA with the peptides increases the hydration of peptides and eventually disrupts the organized morphology of prefibrillar aggregates. It reduces the dimer dissociation energy by -24.34 kJ/mol.
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Affiliation(s)
- Bratin Kumar Das
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore 575025, India
| | - Omkar Singh
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore 575025, India
| | - Debashree Chakraborty
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore 575025, India
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23
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Vargas-Rosales P, D’Addio A, Zhang Y, Caflisch A. Disrupting Dimeric β-Amyloid by Electric Fields. ACS PHYSICAL CHEMISTRY AU 2023; 3:456-466. [PMID: 37780539 PMCID: PMC10540290 DOI: 10.1021/acsphyschemau.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023]
Abstract
The early oligomers of the amyloid Aβ peptide are implicated in Alzheimer's disease, but their transient nature complicates the characterization of their structure and toxicity. Here, we investigate the stability of the minimal toxic species, i.e., β-amyloid dimers, in the presence of an oscillating electric field. We first use deep learning (AlphaFold-multimer) for generating initial models of Aβ42 dimers. The flexibility and secondary structure content of the models are then analyzed by multiple runs of molecular dynamics (MD). Structurally stable models are similar to ensemble representatives from microsecond-long MD sampling. Finally, we employ the validated model as the starting structure of MD simulations in the presence of an external oscillating electric field and observe a fast decay of β-sheet content at high field strengths. Control simulations using the helical dimer of the 42-residue leucine zipper peptide show higher structural stability than the Aβ42 dimer. The simulation results provide evidence that an external electric field (oscillating at 1 GHz) can disrupt amyloid oligomers which should be further investigated by experiments with brain organoids in vitro and eventually in vivo.
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Affiliation(s)
| | - Alessio D’Addio
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Yang Zhang
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
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24
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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25
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Ray S, Mason TO, Boyens-Thiele L, Farzadfard A, Larsen JA, Norrild RK, Jahnke N, Buell AK. Mass photometric detection and quantification of nanoscale α-synuclein phase separation. Nat Chem 2023; 15:1306-1316. [PMID: 37337111 DOI: 10.1038/s41557-023-01244-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023]
Abstract
Protein liquid-liquid phase separation can lead to disease-related amyloid fibril formation. The mechanisms of conversion of monomeric protein into condensate droplets and of the latter into fibrils remain elusive. Here, using mass photometry, we demonstrate that the Parkinson's disease-related protein, α-synuclein, can form dynamic nanoscale clusters at physiologically relevant, sub-saturated concentrations. Nanoclusters nucleate in bulk solution and promote amyloid fibril formation of the dilute-phase monomers upon ageing. Their formation is instantaneous, even under conditions where macroscopic assemblies appear only after several days. The slow growth of the nanoclusters can be attributed to a kinetic barrier, probably due to an interfacial penalty from the charged C terminus of α-synuclein. Our findings reveal that α-synuclein phase separation occurs at much wider ranges of solution conditions than reported so far. Importantly, we establish mass photometry as a promising methodology to detect and quantify nanoscale precursors of phase separation. We also demonstrate its general applicability by probing the existence of nanoclusters of a non-amyloidogenic protein, Ddx4n1.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas O Mason
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Lars Boyens-Thiele
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Azad Farzadfard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jacob Aunstrup Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Rasmus K Norrild
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Nadin Jahnke
- Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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26
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Zhdanov VP. Extracellular interplay of amyloid fibrils and neural cells. Biosystems 2023; 231:104971. [PMID: 37429375 DOI: 10.1016/j.biosystems.2023.104971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023]
Abstract
Some neurological disorders such e.g. as Alzheimer disease are accompanied by the appearance of amyloid fibrils inside and outside cells. Herein, I present a generic coarse-grained kinetic mean-field model describing at the extracellular level the interplay of fibrils and cells. It includes the formation and degradation of fibrils, activation of healthy cells with respect to the fabrication of fibrils, and death of activated cells. The corresponding analysis indicates that the disease development can occur in two qualitatively different regimes. The first one is controlled primarily by the intrinsic factors resulting in slow increase of fibril production inside cells. The second one implies faster self-promoted growth of the fibril population by analogy with explosion. This prediction reported as a hypothesis is of interest for conceptual understanding of the neurological disorders.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Nano and Biophysics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia.
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27
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De Sio S, Waegele J, Bhatia T, Voigt B, Lilie H, Ott M. Inherent Adaptivity of Alzheimer Peptides to Crowded Environments. Macromol Biosci 2023; 23:e2200527. [PMID: 37066978 DOI: 10.1002/mabi.202200527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/30/2023] [Indexed: 04/18/2023]
Abstract
Amyloid β (Aβ) is the major constituent in senile plaques of Alzheimer's disease in which peptides initially undergo structural conversions to form elongated fibrils. The impact of crowding on the fibrillation pathways of Aβ40 and Aβ42 , the most common peptide isoforms are studied. PEG and Ficoll are used as model crowders to mimic a macromolecular enriched surrounding. The fibrillar growth is monitored with the help of ThT-fluorescence assays in order to extract two rates describing primary and secondary processes of nucleation and growth. Techniques as fluorescence correlation spectroscopy and analytical ultracentrifugation are used to discuss oligomeric states; fibril morphologies are investigated using negative-staining transmission electron microscopy. While excluded volume effects imposed by macromolecular crowding are expected to always increase rates of intermolecular interactions and structural conversion, a vast variety of effects are found depending on the peptide, the crowder, or ionic strength of the solution. While investigations of the obtained rates with respect to a reactant-occluded model are capable to display specific surface interactions with the crowder, the employment of crystallization-like models reveal the crowder-induced entropic gain withΔ Δ G fib crow = - 116 ± 21 k $\Delta \Delta G_{\text{fib}}^{\text{crow}}=-116\pm 21\; k$ J mol-1 per volume fraction of the crowder.
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Affiliation(s)
- Silvia De Sio
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Jana Waegele
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Twinkle Bhatia
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Bruno Voigt
- Department of Physics, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Strasse 7, Halle, 06120, Saxony-Anhalt, Germany
| | - Hauke Lilie
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
| | - Maria Ott
- Department of Biotechnology and Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Saxony-Anhalt, Germany
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28
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Nguyen PH, Derreumaux P. Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations. J Chem Phys 2023; 158:235101. [PMID: 37318171 DOI: 10.1063/5.0149419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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29
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Přáda Brichtová E, Krupová M, Bouř P, Lindo V, Gomes Dos Santos A, Jackson SE. Glucagon-like peptide 1 aggregates into low-molecular-weight oligomers off-pathway to fibrillation. Biophys J 2023; 122:2475-2488. [PMID: 37138517 PMCID: PMC10323027 DOI: 10.1016/j.bpj.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/04/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
The physical stability of peptide-based drugs is of great interest to the pharmaceutical industry. Glucagon-like peptide 1 (GLP-1) is a 31-amino acid peptide hormone, the analogs of which are frequently used in the treatment of type 2 diabetes. We investigated the physical stability of GLP-1 and its C-terminal amide derivative, GLP-1-Am, both of which aggregate into amyloid fibrils. While off-pathway oligomers have been proposed to explain the unusual aggregation kinetics observed previously for GLP-1 under specific conditions, these oligomers have not been studied in any detail. Such states are important as they may represent potential sources of cytotoxicity and immunogenicity. Here, we identified and isolated stable, low-molecular-weight oligomers of GLP-1 and GLP-1-Am, using size-exclusion chromatography. Under the conditions studied, isolated oligomers were shown to be resistant to fibrillation or dissociation. These oligomers contain between two and five polypeptide chains and they have a highly disordered structure as indicated by a variety of spectroscopic techniques. They are highly stable with respect to time, temperature, or agitation despite their noncovalent character, which was established using liquid chromatography-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results provide evidence of stable, low-molecular-weight oligomers that are formed by an off-pathway mechanism which competes with amyloid fibril formation.
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Affiliation(s)
- Eva Přáda Brichtová
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Monika Krupová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic; Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic
| | - Viv Lindo
- AstraZeneca, Cambridge, United Kingdom
| | | | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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30
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Jeon J, Yau WM, Tycko R. Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering. Nat Commun 2023; 14:2964. [PMID: 37221174 DOI: 10.1038/s41467-023-38494-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland/National Institute of Standards and Technology, Rockville, MD, 20850, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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31
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Limbocker R, Cremades N, Cascella R, Tessier PM, Vendruscolo M, Chiti F. Characterization of Pairs of Toxic and Nontoxic Misfolded Protein Oligomers Elucidates the Structural Determinants of Oligomer Toxicity in Protein Misfolding Diseases. Acc Chem Res 2023. [PMID: 37071750 DOI: 10.1021/acs.accounts.3c00045] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
ConspectusThe aberrant misfolding and aggregation of peptides and proteins into amyloid aggregates occurs in over 50 largely incurable protein misfolding diseases. These pathologies include Alzheimer's and Parkinson's diseases, which are global medical emergencies owing to their prevalence in increasingly aging populations worldwide. Although the presence of mature amyloid aggregates is a hallmark of such neurodegenerative diseases, misfolded protein oligomers are increasingly recognized as of central importance in the pathogenesis of many of these maladies. These oligomers are small, diffusible species that can form as intermediates in the amyloid fibril formation process or be released by mature fibrils after they are formed. They have been closely associated with the induction of neuronal dysfunction and cell death. It has proven rather challenging to study these oligomeric species because of their short lifetimes, low concentrations, extensive structural heterogeneity, and challenges associated with producing stable, homogeneous, and reproducible populations. Despite these difficulties, investigators have developed protocols to produce kinetically, chemically, or structurally stabilized homogeneous populations of protein misfolded oligomers from several amyloidogenic peptides and proteins at experimentally ameneable concentrations. Furthermore, procedures have been established to produce morphologically similar but structurally distinct oligomers from the same protein sequence that are either toxic or nontoxic to cells. These tools offer unique opportunities to identify and investigate the structural determinants of oligomer toxicity by a close comparative inspection of their structures and the mechanisms of action through which they cause cell dysfunction.This Account reviews multidisciplinary results, including from our own groups, obtained by combining chemistry, physics, biochemistry, cell biology, and animal models for pairs of toxic and nontoxic oligomers. We describe oligomers comprised of the amyloid-β peptide, which underlie Alzheimer's disease, and α-synuclein, which are associated with Parkinson's disease and other related neurodegenerative pathologies, collectively known as synucleinopathies. Furthermore, we also discuss oligomers formed by the 91-residue N-terminal domain of [NiFe]-hydrogenase maturation factor from E. coli, which we use as a model non-disease-related protein, and by an amyloid stretch of Sup35 prion protein from yeast. These oligomeric pairs have become highly useful experimental tools for studying the molecular determinants of toxicity characteristic of protein misfolding diseases. Key properties have been identified that differentiate toxic from nontoxic oligomers in their ability to induce cellular dysfunction. These characteristics include solvent-exposed hydrophobic regions, interactions with membranes, insertion into lipid bilayers, and disruption of plasma membrane integrity. By using these properties, it has been possible to rationalize in model systems the responses to pairs of toxic and nontoxic oligomers. Collectively, these studies provide guidance for the development of efficacious therapeutic strategies to target rationally the cytotoxicity of misfolded protein oligomers in neurodegenerative conditions.
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Affiliation(s)
- Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, New York 10996, United States
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza 50009, Spain
| | - Roberta Cascella
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Peter M Tessier
- Departments of Chemical Engineering, Pharmaceutical Sciences, and Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
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32
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Ezzat K, Sturchio A, Espay AJ. The shift to a proteinopenia paradigm in neurodegeneration. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:23-32. [PMID: 36803814 DOI: 10.1016/b978-0-323-85555-6.00001-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The toxic proteinopathy paradigm has defined neurodegenerative disorders for over a century. This gain-of-function (GOF) framework posited that proteins become toxic when turned into amyloids (pathology), predicting that lowering its levels would translate into clinical benefits. Genetic observations used to support a GOF framework are equally compatible with a loss-of-function (LOF) framework, as the soluble pool of proteins rendered unstable by these mutations (e.g., APP in Alzheimer's disease, SNCA in Parkinson's disease) aggregate, becoming depleted. In this review, we highlight misconceptions that have prevented LOF from gaining currency. Some of these misconceptions include no phenotype in knock-out animals (there is neurodegenerative phenotype in knock-out animals) and high levels of proteins in patients (patients have lower levels of the proteins involved in neurodegeneration than healthy age-matched controls). We also expose the internal contradictions within the GOF framework, namely that (1) pathology can have both pathogenic and protective roles; (2) the neuropathology gold standard for diagnosis can be present in normal individuals and absent in those affected; (3) oligomers are the toxic species even if they are ephemeral and decrease over time. We therefore advocate for a paradigm shift from proteinopathy (GOF) to proteinopenia (LOF) based on the universal depletion of soluble functional proteins in neurodegenerative diseases (low amyloid-β 42 in Alzheimer's disease, low α-synuclein in Parkinson's disease, and low tau in progressive supranuclear palsy) and supported by the confluence of biologic, thermodynamic, and evolutionary principles with proteins having evolved to perform a function, not to become toxic, and where protein depletion is consequential. Such shift to a Proteinopenia paradigm is necessary to examining the safety and efficacy of protein replacement strategies instead of perpetuating a therapeutic paradigm with further antiprotein permutations.
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Affiliation(s)
- Kariem Ezzat
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Andrea Sturchio
- Department of Clinical Neuroscience, Neuro Svenningsson, Karolinska Institutet, Stockholm, Sweden; James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
| | - Alberto J Espay
- James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, Cincinnati, OH, United States
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33
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Yi Y, Lim MH. Current understanding of metal-dependent amyloid-β aggregation and toxicity. RSC Chem Biol 2023; 4:121-131. [PMID: 36794021 PMCID: PMC9906324 DOI: 10.1039/d2cb00208f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022] Open
Abstract
The discovery of effective therapeutics targeting amyloid-β (Aβ) aggregates for Alzheimer's disease (AD) has been very challenging, which suggests its complicated etiology associated with multiple pathogenic elements. In AD-affected brains, highly concentrated metals, such as copper and zinc, are found in senile plaques mainly composed of Aβ aggregates. These metal ions are coordinated to Aβ and affect its aggregation and toxicity profiles. In this review, we illustrate the current view on molecular insights into the assembly of Aβ peptides in the absence and presence of metal ions as well as the effect of metal ions on their toxicity.
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Affiliation(s)
- Yelim Yi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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34
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Cerón R, Peimbert M, Rojo-Domínguez A, Nájera H. Hen lysozyme fibrillogenesis, molten globule intermediate and effect of copper salts. J Biomol Struct Dyn 2023; 41:423-434. [PMID: 34821199 DOI: 10.1080/07391102.2021.2006090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The amyloid fibres have been related to many diseases. The molten globule intermediate has been proposed to form part of the folding pathway of many proteins. In the present study, we investigated the mechanism of amyloid-fibres formation of hen egg-white lysozyme (HEWL) incubated in a potassium phosphate buffer, pH 11.8, 100 mM, at 37 °C for 30 h, and evaluated the influence of Cu(II) present in two salts (CuSO4 and CuCl2) during fibrillogenesis. Co-incubation and post-incubation of lysozyme with copper salts reduced the fluorescence signal of thioflavin T with an increment in the intrinsic fluorescence of the protein. The ANS fluorescence test showed that incubation of HEWL for 6 h generated a molten globule intermediate state that formed amyloid fibres when incubation was carried out for a 30-h timespan. Dynamic light scattering showed a heterogeneous population of states in samples incubated in the absence or the presence of salts during the fibrillation process. The existence of a reducing potential was verified during the formation of HEWL amyloid fibres with the bathocuproine disulphonate test. Transmission electron microscopy confirmed the presence and absence of fibres in solutions incubated with and without Cu(II). This work demonstrated that lysozyme formed amyloid fibres at 37 °C and copper inhibited its formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ricardo Cerón
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico.,Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Arturo Rojo-Domínguez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Hugo Nájera
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
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35
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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36
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Gabriel JM, Tan T, Rinauro DJ, Hsu CM, Buettner CJ, Gilmer M, Kaur A, McKenzie TL, Park M, Cohen S, Errico S, Wright AK, Chiti F, Vendruscolo M, Limbocker R. EGCG inactivates a pore-forming toxin by promoting its oligomerization and decreasing its solvent-exposed hydrophobicity. Chem Biol Interact 2023; 371:110307. [PMID: 36535315 DOI: 10.1016/j.cbi.2022.110307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Natural proteinaceous pore-forming agents can bind and permeabilize cell membranes, leading to ion dyshomeostasis and cell death. In the search for antidotes that can protect cells from peptide toxins, we discovered that the polyphenol epigallocatechin gallate (EGCG) interacts directly with melittin from honeybee venom, resulting in the elimination of its binding to the cell membrane and toxicity by markedly lowering the extent of its solvent-exposed hydrophobicity and promoting its oligomerization into larger species. These physicochemical parameters have also been shown to play a key role in the binding to cells of misfolded protein oligomers in a host of neurodegenerative diseases, where oligomer-membrane binding and associated toxicity have been shown to correlate negatively with oligomer size and positively with solvent-exposed hydrophobicity. For melittin, which is not an amyloid-forming protein and has a very distinct mechanism of toxicity compared to misfolded oligomers, we find that the size-hydrophobicity-toxicity relationship also rationalizes the pharmacological attenuation of melittin toxicity by EGCG. These results highlight the importance of the physicochemical properties of pore forming agents in mediating their interactions with cell membranes and suggest a possible therapeutic approach based on compounds with a similar mechanism of action as EGCG.
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Affiliation(s)
- Justus M Gabriel
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Thomas Tan
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Claire M Hsu
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Caleb J Buettner
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Marshall Gilmer
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Amrita Kaur
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Tristan L McKenzie
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Martin Park
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Sophie Cohen
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Silvia Errico
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK; Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Aidan K Wright
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA.
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37
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O’Day DH. Calmodulin and Amyloid Beta as Coregulators of Critical Events during the Onset and Progression of Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24021393. [PMID: 36674908 PMCID: PMC9863087 DOI: 10.3390/ijms24021393] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/12/2023] Open
Abstract
Calmodulin (CaM) and a diversity of CaM-binding proteins (CaMBPs) are involved in the onset and progression of Alzheimer's disease (AD). In the amyloidogenic pathway, AβPP1, BACE1 and PSEN-1 are all calcium-dependent CaMBPs as are the risk factor proteins BIN1 and TREM2. Ca2+/CaM-dependent protein kinase II (CaMKII) and calcineurin (CaN) are classic CaMBPs involved in memory and plasticity, two events impacted by AD. Coupled with these events is the production of amyloid beta monomers (Aβ) and oligomers (Aβo). The recent revelations that Aβ and Aβo each bind to both CaM and to a host of Aβ receptors that are also CaMBPs adds a new level of complexity to our understanding of the onset and progression of AD. Multiple Aβ receptors that are proven CaMBPs (e.g., NMDAR, PMCA) are involved in calcium homeostasis an early event in AD and other neurodegenerative diseases. Other CaMBPs that are Aβ receptors are AD risk factors while still others are involved in the amyloidogenic pathway. Aβ binding to receptors not only serves to control CaM's ability to regulate critical proteins, but it is also implicated in Aβ turnover. The complexity of the Aβ/CaM/CaMBP interactions is analyzed using two events: Aβ generation and NMDAR function. The interactions between Aβ, CaM and CaMBPs reveals a new level of complexity to critical events associated with the onset and progression of AD and may help to explain the failure to develop successful therapeutic treatments for the disease.
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Affiliation(s)
- Danton H. O’Day
- Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada;
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
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38
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Park S, Na C, Han J, Lim MH. Methods for analyzing the coordination and aggregation of metal-amyloid-β. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2023; 15:6973210. [PMID: 36617236 DOI: 10.1093/mtomcs/mfac102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023]
Abstract
The misfolding and aggregation of amyloid-β (Aβ) peptides are histopathological features found in the brains of Alzheimer's disease (AD). To discover effective therapeutics for AD, numerous efforts have been made to control the aggregation of Aβ species and their interactions with other pathological factors, including metal ions. Metal ions, such as Cu(II) and Zn(II), can bind to Aβ peptides forming metal-bound Aβ (metal-Aβ) complexes and, subsequently, alter their aggregation pathways. In particular, redox-active metal ions bound to Aβ species can produce reactive oxygen species leading to oxidative stress. In this review, we briefly illustrate some experimental approaches for characterizing the coordination and aggregation properties of metal-Aβ complexes.
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Affiliation(s)
- Seongmin Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Chanju Na
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jiyeon Han
- Department of Applied Chemistry, University of Seoul, Seoul 02504, Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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39
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Huang Z. A Function of Amyloid-β in Mediating Activity-Dependent Axon/Synapse Competition May Unify Its Roles in Brain Physiology and Pathology. J Alzheimers Dis 2023; 92:29-57. [PMID: 36710681 PMCID: PMC10023438 DOI: 10.3233/jad-221042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Amyloid-β protein precursor (AβPP) gives rise to amyloid-β (Aβ), a peptide at the center of Alzheimer's disease (AD). AβPP, however, is also an ancient molecule dating back in evolution to some of the earliest forms of metazoans. This suggests a possible ancestral function that may have been obscured by those that evolve later. Based on literature from the functions of Aβ/AβPP in nervous system development, plasticity, and disease, to those of anti-microbial peptides (AMPs) in bacterial competition as well as mechanisms of cell competition uncovered first by Drosophila genetics, I propose that Aβ/AβPP may be part of an ancient mechanism employed in cell competition, which is subsequently co-opted during evolution for the regulation of activity-dependent neural circuit development and plasticity. This hypothesis is supported by foremost the high similarities of Aβ to AMPs, both of which possess unique, opposite (i.e., trophic versus toxic) activities as monomers and oligomers. A large body of data further suggests that the different Aβ oligomeric isoforms may serve as the protective and punishment signals long predicted to mediate activity-dependent axonal/synaptic competition in the developing nervous system and that the imbalance in their opposite regulation of innate immune and glial cells in the brain may ultimately underpin AD pathogenesis. This hypothesis can not only explain the diverse roles observed of Aβ and AβPP family molecules, but also provide a conceptual framework that can unify current hypotheses on AD. Furthermore, it may explain major clinical observations not accounted for and identify approaches for overcoming shortfalls in AD animal modeling.
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Affiliation(s)
- Zhen Huang
- Departments of Neuroscience and Neurology, University of Wisconsin-Madison, Madison, WI, USA
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40
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Wu K, Sun W, Li D, Diao J, Xiu P. Inhibition of Amyloid Nucleation by Steric Hindrance. J Phys Chem B 2022; 126:10045-10054. [PMID: 36417323 DOI: 10.1021/acs.jpcb.2c06330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite recent experiments and simulations suggesting that small-molecule inhibitors and some post-translational modifications (e.g., glycosylation and ubiquitination) can suppress the pathogenic aggregation of proteins due to steric hindrance, the effect of steric hindrance on amyloid formation has not been systematically studied. Based on Monte Carlo simulations using a coarse-grained model for amyloidogenic proteins and a hard sphere acting as steric hindrance, we investigated how steric hindrance on proteins could affect amyloid formation, particularly two steps of primary nucleation, namely, oligomerization and conformational conversion into a β-sheet-enriched nucleus. We found that steric spheres played an inhibitory role in oligomerization with the effect proportional to the sphere radius RS, which we attributed to the decline in the nonspecific attractions between proteins. During the second step, small steric spheres facilitated the conformational conversion of proteins while large ones suppressed the conversion. The overall steric effect on amyloid nucleation was inhibitory regardless of RS. As RS increased, oligomeric assemblies changed from amorphous into sheet-like, structurally ordered species, reminiscent of the structure of amyloid fibrils. The oligomers with large RS were off-pathway with their ordered structures induced by the competition between steric hindrance and nonspecific attractions of soluble proteins. Interestingly, the equimolar mixture of proteins with and without steric hindrance amplified the sterically inhibitory effect by increasing the energy barrier of protein's conformational conversion. The physical mechanisms and biological implications of the above results are discussed. Our findings improve the current understanding of how nature regulates protein aggregation and amyloid formation by steric hindrance.
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Affiliation(s)
- Kai Wu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Wuxuepeng Sun
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Dechang Li
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Peng Xiu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
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41
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Bortoletto AS, Graham WV, Trout G, Bonito‐Oliva A, Kazmi MA, Gong J, Weyburne E, Houser BL, Sakmar TP, Parchem RJ. Human Islet Amyloid Polypeptide (hIAPP) Protofibril-Specific Antibodies for Detection and Treatment of Type 2 Diabetes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202342. [PMID: 36257905 PMCID: PMC9731688 DOI: 10.1002/advs.202202342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/26/2022] [Indexed: 05/27/2023]
Abstract
Type 2 diabetes mellitus (T2D) is a major public health concern and is characterized by sustained hyperglycemia due to insulin resistance and destruction of insulin-producing β cells. One pathological hallmark of T2D is the toxic accumulation of human islet amyloid polypeptide (hIAPP) aggregates. Monomeric hIAPP is a hormone normally co-secreted with insulin. However, increased levels of hIAPP in prediabetic and diabetic patients can lead to the formation of hIAPP protofibrils, which are toxic to β cells. Current therapies fail to address hIAPP aggregation and current screening modalities do not detect it. Using a stabilizing capping protein, monoclonal antibodies (mAbs) can be developed against a previously nonisolatable form of hIAPP protofibrils, which are protofibril specific and do not engage monomeric hIAPP. Shown here are two candidate mAbs that can detect hIAPP protofibrils in serum and hIAPP deposits in pancreatic islets in a mouse model of rapidly progressing T2D. Treatment of diabetic mice with the mAbs delays disease progression and dramatically increases overall survival. These results demonstrate the potential for using novel hIAPP protofibril-specific mAbs as a diagnostic screening tool for early detection of T2D, as well as therapeutically to preserve β cell function and target one of the underlying pathological mechanisms of T2D.
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Affiliation(s)
- Angelina S. Bortoletto
- Center for Cell and Gene TherapyStem Cells and Regenerative Medicine CenterDepartment of NeuroscienceDepartment of Molecular and Cellular BiologyTranslational Biology and Molecular Medicine ProgramMedical Scientist Training ProgramBaylor College of MedicineOne Baylor PlazaHoustonTX77030USA
| | - W. Vallen Graham
- Laboratory of Chemical Biology & Signal TransductionThe Rockefeller University1230 York AvenueNew YorkNY10065USA
| | - Gabriella Trout
- Center for Cell and Gene TherapyStem Cells and Regenerative Medicine CenterDepartment of NeuroscienceDepartment of Molecular and Cellular BiologyTranslational Biology and Molecular Medicine ProgramMedical Scientist Training ProgramBaylor College of MedicineOne Baylor PlazaHoustonTX77030USA
| | - Alessandra Bonito‐Oliva
- Laboratory of Chemical Biology & Signal TransductionThe Rockefeller University1230 York AvenueNew YorkNY10065USA
| | - Manija A. Kazmi
- Laboratory of Chemical Biology & Signal TransductionThe Rockefeller University1230 York AvenueNew YorkNY10065USA
| | - Jing Gong
- Celdara Medical16 Cavendish CourtLebanonNH03766USA
| | | | | | - Thomas P. Sakmar
- Laboratory of Chemical Biology & Signal TransductionThe Rockefeller University1230 York AvenueNew YorkNY10065USA
- Department of Neurobiology, Care Sciences, and SocietyCenter for Alzheimer ResearchDivision of NeurogeriatricsKarolinska InstitutetSolna17164Sweden
| | - Ronald J. Parchem
- Center for Cell and Gene TherapyStem Cells and Regenerative Medicine CenterDepartment of NeuroscienceDepartment of Molecular and Cellular BiologyTranslational Biology and Molecular Medicine ProgramMedical Scientist Training ProgramBaylor College of MedicineOne Baylor PlazaHoustonTX77030USA
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42
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Prosswimmer T, Daggett V. The role of α-sheet structure in amyloidogenesis: characterization and implications. Open Biol 2022; 12:220261. [PMID: 36416010 PMCID: PMC9682440 DOI: 10.1098/rsob.220261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Amyloid diseases are linked to protein misfolding whereby the amyloidogenic protein undergoes a conformational change, aggregates and eventually forms amyloid fibrils. While the amyloid fibrils and plaques are hallmarks of these diseases, they typically form late in the disease process and do not correlate with disease. Instead, there is growing evidence that smaller, soluble toxic oligomers form prior and appear to be early triggers of the molecular pathology underlying these diseases. Nearly 20 years ago, we proposed the α-sheet hypothesis after discovering that the early conformational changes observed during atomistic molecular dynamics simulations involve the formation of a non-standard protein structure, α-sheet. Furthermore, we proposed that toxic oligomers contain α-sheet structure and that preferentially targeting this structure could neutralize the toxicity, prevent further aggregation and serve as the basis for early detection of disease. Here, we present the origin of the α-sheet hypothesis and describe α-sheet structure and the corresponding mechanisms of conversion. We discuss experimental studies demonstrating that both mammalian and bacterial amyloid systems form α-sheet oligomers before converting to conventional β-sheet fibrils. Furthermore, we show that the process can be inhibited with de novo designed α-sheet peptides complementary to the structure in the toxic oligomers.
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Affiliation(s)
- Tatum Prosswimmer
- Molecular Engineering Program, University of Washington, Seattle, WA 98195-5013, USA
| | - Valerie Daggett
- Molecular Engineering Program, University of Washington, Seattle, WA 98195-5013, USA,Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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43
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Bell R, Thrush RJ, Castellana-Cruz M, Oeller M, Staats R, Nene A, Flagmeier P, Xu CK, Satapathy S, Galvagnion C, Wilson MR, Dobson CM, Kumita JR, Vendruscolo M. N-Terminal Acetylation of α-Synuclein Slows down Its Aggregation Process and Alters the Morphology of the Resulting Aggregates. Biochemistry 2022; 61:1743-1756. [PMID: 35944093 PMCID: PMC9454101 DOI: 10.1021/acs.biochem.2c00104] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Parkinson’s disease is associated with the aberrant
aggregation
of α-synuclein. Although the causes of this process are still
unclear, post-translational modifications of α-synuclein are
likely to play a modulatory role. Since α-synuclein is constitutively
N-terminally acetylated, we investigated how this post-translational
modification alters the aggregation behavior of this protein. By applying
a three-pronged aggregation kinetics approach, we observed that N-terminal
acetylation results in a reduced rate of lipid-induced aggregation
and slows down both elongation and fibril-catalyzed aggregate proliferation.
An analysis of the amyloid fibrils produced by the aggregation process
revealed different morphologies for the acetylated and non-acetylated
forms in both lipid-induced aggregation and seed-induced aggregation
assays. In addition, we found that fibrils formed by acetylated α-synuclein
exhibit a lower β-sheet content. These findings indicate that
N-terminal acetylation of α-synuclein alters its lipid-dependent
aggregation behavior, reduces its rate of in vitro aggregation, and
affects the structural properties of its fibrillar aggregates.
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Affiliation(s)
- Rosie Bell
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Rebecca J Thrush
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Marta Castellana-Cruz
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Marc Oeller
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Roxine Staats
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Aishwarya Nene
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Patrick Flagmeier
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Catherine K Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Sandeep Satapathy
- Department of Cell Biology, Blavantik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Celine Galvagnion
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Mark R Wilson
- School of Chemistry and Molecular Bioscience, Molecular Horizons Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Janet R Kumita
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, U.K
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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Lauth LM, Voigt B, Bhatia T, Machner L, Balbach J, Ott M. Heparin promotes rapid fibrillation of the basic Parathyroid Hormone at physiological pH. FEBS Lett 2022; 596:2928-2939. [PMID: 35903816 DOI: 10.1002/1873-3468.14455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/14/2022] [Accepted: 07/09/2022] [Indexed: 11/06/2022]
Abstract
In acidic secretory granules of mammalian cells, peptide hormones including the parathyroid hormone (PTH) are presumably stored in the form of functional amyloid fibrils. Mature PTH, however, is considerably positively charged in acidic environments, a condition known to impede unassisted self-aggregation into fibrils. Here, we studied the role of the polyanion heparin on promoting fibril formation of PTH. Employing ITC, CD spectroscopy, NMR, SAXS and fluorescence-based assays we could demonstrate that heparin binds PTH with submicromolar affinity and facilitates its conversion into fibrillar seeds, enabling rapid formation of amyloid fibrils under acidic conditions. In absence of heparin, PTH remained in a soluble monomeric state. We suspect that heparin-like surfaces are required in vivo to convert PTH efficiently into fibrillar deposits.
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Affiliation(s)
- Luca M Lauth
- Department of Biochemistry and Biotechnology, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
| | - Bruno Voigt
- Department of Biophysics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Twinkle Bhatia
- Department of Biochemistry and Biotechnology, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
| | - Lisa Machner
- Department of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Jochen Balbach
- Department of Biophysics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Maria Ott
- Department of Biochemistry and Biotechnology, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
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Catalini S, Lutz-Bueno V, Usuelli M, Diener M, Taschin A, Bartolini P, Foggi P, Paolantoni M, Mezzenga R, Torre R. Multi-length scale structural investigation of lysozyme self-assembly. iScience 2022; 25:104586. [PMID: 35784788 PMCID: PMC9240868 DOI: 10.1016/j.isci.2022.104586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Reactive amyloid oligomers are responsible for cytotoxicity in amyloid pathologies and because of their unstable nature characterizing their behavior is a challenge. The physics governing the self-assembly of proteins in crowded conditions is extremely complex and its comprehension, despite its paramount relevance to understanding molecular mechanisms inside cells and optimizing pharmaceutical processes, remains inconclusive. Here, we focus on the amyloid oligomerization process in self-crowded lysozyme aqueous solutions in acidic conditions. We reveal that the amyloid oligomers form at high protein concentration and low pH. Through multi-length scale spectroscopic investigations, we find that amyloid oligomers can further interconnect with each other by weak and non-specific interactions forming an extended network that leads to the percolation of the whole system. Our multi-length scale structural analysis follows the thermal history of amyloid oligomers from different perspectives and highlights the impact of hierarchical self-assembly of biological macromolecules on functional properties. Use of multi-length scale spectroscopies to characterize unstable amyloid oligomers Lysozyme form thermo-labile amyloid oligomers in self-crowded conditions Amyloid oligomers interact and form an extended hydrogel network Amyloid oligomers are responsible for the existence of the hydrogel matrix
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46
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Meisl G, Knowles TPJ, Klenerman D. Mechanistic Models of Protein Aggregation Across Length-Scales and Time-Scales: From the Test Tube to Neurodegenerative Disease. Front Neurosci 2022; 16:909861. [PMID: 35844223 PMCID: PMC9281552 DOI: 10.3389/fnins.2022.909861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022] Open
Abstract
Through advances in the past decades, the central role of aberrant protein aggregation has been established in many neurodegenerative diseases. Crucially, however, the molecular mechanisms that underlie aggregate proliferation in the brains of affected individuals are still only poorly understood. Under controlled in vitro conditions, significant progress has been made in elucidating the molecular mechanisms that take place during the assembly of purified protein molecules, through advances in both experimental methods and the theories used to analyse the resulting data. The determination of the aggregation mechanism for a variety of proteins revealed the importance of intermediate oligomeric species and of the interactions with promotors and inhibitors. Such mechanistic insights, if they can be achieved in a disease-relevant system, provide invaluable information to guide the design of potential cures to these devastating disorders. However, as experimental systems approach the situation present in real disease, their complexity increases substantially. Timescales increase from hours an aggregation reaction takes in vitro, to decades over which the process takes place in disease, and length-scales increase to the dimension of a human brain. Thus, molecular level mechanistic studies, like those that successfully determined mechanisms in vitro, have only been applied in a handful of living systems to date. If their application can be extended to further systems, including patient data, they promise powerful new insights. Here we present a review of the existing strategies to gain mechanistic insights into the molecular steps driving protein aggregation and discuss the obstacles and potential paths to achieving their application in disease. First, we review the experimental approaches and analysis techniques that are used to establish the aggregation mechanisms in vitro and the insights that have been gained from them. We then discuss how these approaches must be modified and adapted to be applicable in vivo and review the existing works that have successfully applied mechanistic analysis of protein aggregation in living systems. Finally, we present a broad mechanistic classification of in vivo systems and discuss what will be required to further our understanding of aggregate formation in living systems.
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Affiliation(s)
- Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- UK Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom
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Sun X, Ferguson JA, Dyson HJ, Wright PE. A transthyretin monomer intermediate undergoes local unfolding and transient interaction with oligomers in a kinetically concerted aggregation pathway. J Biol Chem 2022; 298:102162. [PMID: 35724960 PMCID: PMC9293765 DOI: 10.1016/j.jbc.2022.102162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/15/2022] Open
Abstract
Transthyretin (TTR) amyloidosis is associated with tissue deposition of TTR aggregates. TTR aggregation is initiated by dissociation of the native tetramer to form a monomeric intermediate, which locally unfolds and assembles into soluble oligomers and higher-order aggregates. However, a detailed mechanistic understanding requires kinetic and structural characterization of the low-population intermediates formed. Here we show that the monomeric intermediate exchanges with an ensemble of oligomers on the millisecond timescale. This transient and reversible exchange causes broadening of the 19F resonance of a trifluoromethyl probe coupled to the monomeric intermediate at S85C. We show the 19F linewidth and R2 relaxation rate increase in a linear manner with increasing concentration of the oligomer. Furthermore, introduction of 19F probes at additional TTR sites yielded distinct 19F chemical shifts for the TTR tetramer and monomer when the trifluoromethyl probe was attached at S100C, located near the same subunit interface as S85C, but not with probes attached at S46C or E63C, which are distant from any interfaces. The 19F probe at E63C shows that part of the DE loop, which is solvent-accessible in the tetramer, becomes more buried in the NMR-visible oligomers. Finally, using backbone amides as probes, we show that parts of the EF helix and H strand become highly flexible in the otherwise structured monomeric intermediate at acidic pH. We further find that TTR aggregation can be reversed by increasing pH. Taken together, this work provides insights into location-dependent conformational changes in the reversible early steps of a kinetically-concerted TTR aggregation pathway.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - James A Ferguson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
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48
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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Sanchez-Varo R, Mejias-Ortega M, Fernandez-Valenzuela JJ, Nuñez-Diaz C, Caceres-Palomo L, Vegas-Gomez L, Sanchez-Mejias E, Trujillo-Estrada L, Garcia-Leon JA, Moreno-Gonzalez I, Vizuete M, Vitorica J, Baglietto-Vargas D, Gutierrez A. Transgenic Mouse Models of Alzheimer's Disease: An Integrative Analysis. Int J Mol Sci 2022; 23:5404. [PMID: 35628216 PMCID: PMC9142061 DOI: 10.3390/ijms23105404] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/10/2022] [Indexed: 12/16/2022] Open
Abstract
Alzheimer's disease (AD) constitutes the most prominent form of dementia among elderly individuals worldwide. Disease modeling using murine transgenic mice was first initiated thanks to the discovery of heritable mutations in amyloid precursor protein (APP) and presenilins (PS) genes. However, due to the repeated failure of translational applications from animal models to human patients, along with the recent advances in genetic susceptibility and our current understanding on disease biology, these models have evolved over time in an attempt to better reproduce the complexity of this devastating disease and improve their applicability. In this review, we provide a comprehensive overview about the major pathological elements of human AD (plaques, tauopathy, synaptic damage, neuronal death, neuroinflammation and glial dysfunction), discussing the knowledge that available mouse models have provided about the mechanisms underlying human disease. Moreover, we highlight the pros and cons of current models, and the revolution offered by the concomitant use of transgenic mice and omics technologies that may lead to a more rapid improvement of the present modeling battery.
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Affiliation(s)
- Raquel Sanchez-Varo
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Fisiologia Humana, Histologia Humana, Anatomia Patologica y Educacion Fisica y Deportiva, Facultad de Medicina, Universidad de Malaga, 29071 Malaga, Spain
| | - Marina Mejias-Ortega
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Juan Jose Fernandez-Valenzuela
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Cristina Nuñez-Diaz
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Caceres-Palomo
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Vegas-Gomez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Elisabeth Sanchez-Mejias
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Laura Trujillo-Estrada
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Juan Antonio Garcia-Leon
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Ines Moreno-Gonzalez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Marisa Vizuete
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBIS)-Hospital Universitario Virgen del Rocio/CSIC, 41012 Seville, Spain
| | - Javier Vitorica
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
- Departamento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBIS)-Hospital Universitario Virgen del Rocio/CSIC, 41012 Seville, Spain
| | - David Baglietto-Vargas
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
| | - Antonia Gutierrez
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain; (R.S.-V.); (M.M.-O.); (J.J.F.-V.); (C.N.-D.); (L.C.-P.); (L.V.-G.); (E.S.-M.); (L.T.-E.); (J.A.G.-L.); (I.M.-G.)
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain; (M.V.); (J.V.)
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50
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Michaels TCT, Dear AJ, Cohen SIA, Vendruscolo M, Knowles TPJ. Kinetic profiling of therapeutic strategies for inhibiting the formation of amyloid oligomers. J Chem Phys 2022; 156:164904. [PMID: 35490011 DOI: 10.1063/5.0077609] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein self-assembly into amyloid fibrils underlies several neurodegenerative conditions, including Alzheimer's and Parkinson's diseases. It has become apparent that the small oligomers formed during this process constitute neurotoxic molecular species associated with amyloid aggregation. Targeting the formation of oligomers represents, therefore, a possible therapeutic avenue to combat these diseases. However, it remains challenging to establish which microscopic steps should be targeted to suppress most effectively the generation of oligomeric aggregates. Recently, we have developed a kinetic model of oligomer dynamics during amyloid aggregation. Here, we use this approach to derive explicit scaling relationships that reveal how key features of the time evolution of oligomers, including oligomer peak concentration and lifetime, are controlled by the different rate parameters. We discuss the therapeutic implications of our framework by predicting changes in oligomer concentrations when the rates of the individual microscopic events are varied. Our results identify the kinetic parameters that control most effectively the generation of oligomers, thus opening a new path for the systematic rational design of therapeutic strategies against amyloid-related diseases.
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Affiliation(s)
- Thomas C T Michaels
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Alexander J Dear
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Samuel I A Cohen
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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