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Pagano K, De Rosa L, Tomaselli S, Molinari H, D'Andrea LD, Ragona L. Characterizing the Oligomers Distribution along the Aggregation Pathway of Amyloid Aβ1-40 by NMR. Chemistry 2024; 30:e202400594. [PMID: 38712990 DOI: 10.1002/chem.202400594] [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: 02/13/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
This study delves into the early aggregation process of the Aβ1-40 amyloid peptide, elucidating the associated oligomers distribution. Motivated by the acknowledged role of small oligomers in the neurotoxic damage linked to Alzheimer's disease, we present an experimental protocol for preparing 26-O-acyl isoAβ1-40, a modified Aβ1-40 peptide facilitating rapid isomerization to the native amide form at neutral pH. This ensures seed-free solutions, minimizing experimental variability. Additionally, we demonstrate the efficacy of coupling NMR diffusion ordered spectroscopy (DOSY) with the Inverse Laplace Transform (ILT) reconstruction method, for effective characterization of early aggregation processes. This innovative approach efficiently maps oligomers distributions across a wide spectrum of initial peptide concentrations offering unique insights into the evolution of oligomers relative populations. As a proof of concept, we demonstrate the efficacy of our approach assessing the impact of Epigallocathechin gallate, a known remodeling agent of amyloid fibrils, on the oligomeric distributions of aggregated Aβ1-40. The DOSY-ILT proposed approach stands as a robust and discriminating asset, providing a powerful strategy for rapidly gaining insight into potential inhibitors' impact on the aggregation process.
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Affiliation(s)
- Katiuscia Pagano
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini CNR, Via Pietro Castellino 111, Napoli, Italy
| | - Simona Tomaselli
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Henriette Molinari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Luca Domenico D'Andrea
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, Via Mario Bianco, 9, Milano, Italy
| | - Laura Ragona
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
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2
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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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3
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Sarkar D, Saha S, Krishnamoorthy J, Bhunia A. Application of singular value decomposition analysis: Insights into the complex mechanisms of amyloidogenesis. Biophys Chem 2024; 306:107157. [PMID: 38184980 DOI: 10.1016/j.bpc.2023.107157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Amyloidogenesis, with its multifaceted nature spanning from peptide self-assembly to membrane-mediated structural transitions, presents a significant challenge for the interdisciplinary scientific community. Here, we emphasize on how Singular Value Decomposition (SVD) can be employed to reveal hidden patterns and dominant modes of interaction that govern the complex process of amyloidogenesis. We first utilize SVD analysis on Circular Dichroism (CD) spectral datasets to identify the intermediate structural species emerging during peptide-membrane interactions and to determine binding constants more precisely than conventional methods. We investigate the monomer loss kinetics associated with peptide self-assembly using Nuclear Magnetic Resonance (NMR) dataset and determine the global kinetic parameters through SVD. Furthermore, we explore the seeded growth of amyloid fibrils by analyzing a time-dependent NMR dataset, shedding light on the kinetic intricacies of this process. Our analysis uncovers two distinct states in the aggregation of Aβ40 and pinpoints key residues responsible for this seeded growth. To strengthen our findings and enhance their robustness, we validate those using simulated data, thereby highlighting the physical interpretations derived from SVD. Overall, SVD analysis offers a model-free, global kinetic perspective, enabling the selection of optimal kinetic models. This study not only contributes valuable insights into the dynamics but also highlights the versatility of SVD in unravelling complex processes of amyloidogenesis.
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Affiliation(s)
- Dibakar Sarkar
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake, Sector V, Kolkata 700 091, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Unified Academic Campus, Salt Lake, Sector V, Kolkata 700 091, India
| | | | - Anirban Bhunia
- Department of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake, Sector V, Kolkata 700 091, India.
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Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Mol Biol Cell 2024; 35:mr1. [PMID: 38117593 PMCID: PMC10916857 DOI: 10.1091/mbc.e23-07-0289] [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: 08/07/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/22/2023] Open
Abstract
The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt.
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Affiliation(s)
- Zsuzsa Sárkány
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Francisco Figueiredo
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Pedro M. Martins
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
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Gardon L, Becker N, Rähse N, Hölbling C, Apostolidis A, Schulz CM, Bochinsky K, Gremer L, Heise H, Lakomek NA. Amyloid fibril formation kinetics of low-pH denatured bovine PI3K-SH3 monitored by three different NMR techniques. Front Mol Biosci 2023; 10:1254721. [PMID: 38046811 PMCID: PMC10691488 DOI: 10.3389/fmolb.2023.1254721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
Introduction: Misfolding of amyloidogenic proteins is a molecular hallmark of neurodegenerative diseases in humans. A detailed understanding of the underlying molecular mechanisms is mandatory for developing innovative therapeutic approaches. The bovine PI3K-SH3 domain has been a model system for aggregation and fibril formation. Methods: We monitored the fibril formation kinetics of low pH-denatured recombinantly expressed [U-13C, 15N] labeled bovine PI3K-SH3 by a combination of solution NMR, high-resolution magic angle spinning (HR-MAS) NMR and solid-state NMR spectra. Solution NMR offers the highest sensitivity and, therefore, allows for the recording of two-dimensional NMR spectra with residue-specific resolution for individual time points of the time series. However, it can only follow the decay of the aggregating monomeric species. In solution NMR, aggregation occurs under quiescent experimental conditions. Solid-state NMR has lower sensitivity and allows only for the recording of one-dimensional spectra during the time series. Conversely, solid-state NMR is the only technique to detect disappearing monomers and aggregated species in the same sample by alternatingly recoding scalar coupling and dipolar coupling (CP)-based spectra. HR-MAS NMR is used here as a hybrid method bridging solution and solid-state NMR. In solid-state NMR and HR-MAS NMR the sample is agitated due to magic angle spinning. Results: Good agreement of the decay rate constants of monomeric SH3, measured by the three different NMR methods, is observed. Moderate MAS up to 8 kHz seems to influence the aggregation kinetics of seeded fibril formation only slightly. Therefore, under sufficient seeding (1% seeds used here), quiescent conditions (solution NMR), and agitated conditions deliver similar results, arguing against primary nucleation induced by MAS as a major contributor. Using solid-state NMR, we find that the amount of disappeared monomer corresponds approximately to the amount of aggregated species under the applied experimental conditions (250 µM PI3K-SH3, pH 2.5, 298 K, 1% seeds) and within the experimental error range. Data can be fitted by simple mono-exponential conversion kinetics, with lifetimes τ in the 14-38 h range. Atomic force microscopy confirms that fibrils substantially grew in length during the aggregation experiment. This argues for fibril elongation as the dominant growth mechanism in fibril mass (followed by the CP-based solid-state NMR signal). Conclusion: We suggest a combined approach employing both solution NMR and solid-state NMR, back-to-back, on two aliquots of the same sample under seeding conditions as an additional approach to follow monomer depletion and growth of fibril mass simultaneously. Atomic force microscopy images confirm fibril elongation as a major contributor to the increase in fibril mass.
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Affiliation(s)
- Luis Gardon
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nina Becker
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nick Rähse
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Christoph Hölbling
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Athina Apostolidis
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Celina M. Schulz
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Kevin Bochinsky
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nils-Alexander Lakomek
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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6
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Bellomo G, Paciotti S, Concha-Marambio L, Rizzo D, Wojdaƚa AL, Chiasserini D, Gatticchi L, Cerofolini L, Giuntini S, De Luca CMG, Ma Y, Farris CM, Pieraccini G, Bologna S, Filidei M, Ravera E, Lelli M, Moda F, Fragai M, Parnetti L, Luchinat C. Cerebrospinal fluid lipoproteins inhibit α-synuclein aggregation by interacting with oligomeric species in seed amplification assays. Mol Neurodegener 2023; 18:20. [PMID: 37005644 PMCID: PMC10068178 DOI: 10.1186/s13024-023-00613-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/12/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND Aggregation of α-synuclein (α-syn) is a prominent feature of Parkinson's disease (PD) and other synucleinopathies. Currently, α-syn seed amplification assays (SAAs) using cerebrospinal fluid (CSF) represent the most promising diagnostic tools for synucleinopathies. However, CSF itself contains several compounds that can modulate the aggregation of α-syn in a patient-dependent manner, potentially undermining unoptimized α-syn SAAs and preventing seed quantification. METHODS In this study, we characterized the inhibitory effect of CSF milieu on detection of α-syn aggregates by means of CSF fractionation, mass spectrometry, immunoassays, transmission electron microscopy, solution nuclear magnetic resonance spectroscopy, a highly accurate and standardized diagnostic SAA, and different in vitro aggregation conditions to evaluate spontaneous aggregation of α-syn. RESULTS We found the high-molecular weight fraction of CSF (> 100,000 Da) to be highly inhibitory on α-syn aggregation and identified lipoproteins to be the main drivers of this effect. Direct interaction between lipoproteins and monomeric α-syn was not detected by solution nuclear magnetic resonance spectroscopy, on the other hand we observed lipoprotein-α-syn complexes by transmission electron microscopy. These observations are compatible with hypothesizing an interaction between lipoproteins and oligomeric/proto-fibrillary α-syn intermediates. We observed significantly slower amplification of α-syn seeds in PD CSF when lipoproteins were added to the reaction mix of diagnostic SAA. Additionally, we observed a decreased inhibition capacity of CSF on α-syn aggregation after immunodepleting ApoA1 and ApoE. Finally, we observed that CSF ApoA1 and ApoE levels significantly correlated with SAA kinetic parameters in n = 31 SAA-negative control CSF samples spiked with preformed α-syn aggregates. CONCLUSIONS Our results describe a novel interaction between lipoproteins and α-syn aggregates that inhibits the formation of α-syn fibrils and could have relevant implications. Indeed, the donor-specific inhibition of CSF on α-syn aggregation explains the lack of quantitative results from analysis of SAA-derived kinetic parameters to date. Furthermore, our data show that lipoproteins are the main inhibitory components of CSF, suggesting that lipoprotein concentration measurements could be incorporated into data analysis models to eliminate the confounding effects of CSF milieu on α-syn quantification efforts.
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Affiliation(s)
- Giovanni Bellomo
- Laboratory of Clinical Neurochemistry, Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy.
| | - Silvia Paciotti
- Laboratory of Clinical Neurochemistry, Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy
| | - Luis Concha-Marambio
- R&D Unit, Amprion Inc, 11095 Flintkote Av., San Diego, San Diego, CA, 92121, USA
| | - Domenico Rizzo
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Anna Lidia Wojdaƚa
- Laboratory of Clinical Neurochemistry, Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy
| | - Davide Chiasserini
- Section of Physiology and Biochemistry, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, PerugiaPerugia, Italy
| | - Leonardo Gatticchi
- Section of Physiology and Biochemistry, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, PerugiaPerugia, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Chiara Maria Giulia De Luca
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Yihua Ma
- R&D Unit, Amprion Inc, 11095 Flintkote Av., San Diego, San Diego, CA, 92121, USA
| | - Carly M Farris
- R&D Unit, Amprion Inc, 11095 Flintkote Av., San Diego, San Diego, CA, 92121, USA
| | - Giuseppe Pieraccini
- Department of Health Sciences, CISM Mass Spectrometry Centre, University of Florence, Viale Gaetano Pieraccini 6, 50139, Florence, Italy
| | - Sara Bologna
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Marta Filidei
- Laboratory of Clinical Neurochemistry, Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Moreno Lelli
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Fabio Moda
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via Celoria 11, 20133, Milan, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Lucilla Parnetti
- Laboratory of Clinical Neurochemistry, Section of Neurology, Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
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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: 56] [Impact Index Per Article: 56.0] [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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8
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Identification of a human estrogen receptor α tetrapeptidic fragment with dual antiproliferative and anti-nociceptive action. Sci Rep 2023; 13:1326. [PMID: 36693877 PMCID: PMC9873809 DOI: 10.1038/s41598-023-28062-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
The synthetic peptide ERα17p (sequence: PLMIKRSKKNSLALSLT), which corresponds to the 295-311 region of the human estrogen receptor α (ERα), induces apoptosis in breast cancer cells. In mice and at low doses, it promotes not only the decrease of the size of xenografted triple-negative human breast tumors, but also anti-inflammatory and anti-nociceptive effects. Recently, we have shown that these effects were due to its interaction with the seven-transmembrane G protein-coupled estrogen receptor GPER. Following modeling studies, the C-terminus of this peptide (sequence: NSLALSLT) remains compacted at the entrance of the GPER ligand-binding pocket, whereas its N-terminus (sequence: PLMI) engulfs in the depth of the same pocket. Thus, we have hypothesized that the PLMI motif could support the pharmacological actions of ERα17p. Here, we show that the PLMI peptide is, indeed, responsible for the GPER-dependent antiproliferative and anti-nociceptive effects of ERα17p. By using different biophysical approaches, we demonstrate that the NSLALSLT part of ERα17p is responsible for aggregation. Overall, the tetrapeptide PLMI, which supports the action of the parent peptide ERα17p, should be considered as a hit for the synthesis of new GPER modulators with dual antiproliferative and anti-nociceptive actions. This study highlights also the interest to modulate GPER for the control of pain.
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9
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Hutchison MT, Bellomo G, Cherepanov A, Stirnal E, Fürtig B, Richter C, Linhard V, Gurewitsch E, Lelli M, Morgner N, Schrader T, Schwalbe H. Modulation of Aβ42 Aggregation Kinetics and Pathway by Low-Molecular-Weight Inhibitors. Chembiochem 2023; 24:e202200760. [PMID: 36652672 DOI: 10.1002/cbic.202200760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
The aggregation of amyloid-β 42 (Aβ42) is directly related to the pathogenesis of Alzheimer's disease. Here, we have investigated the early stages of the aggregation process, during which most of the cytotoxic species are formed. Aβ42 aggregation kinetics, characterized by the quantification of Aβ42 monomer consumption, were tracked by real-time solution NMR spectroscopy (RT-NMR) allowing the impact that low-molecular-weight (LMW) inhibitors and modulators exert on the aggregation process to be analysed. Distinct differences in the Aβ42 kinetic profiles were apparent and were further investigated kinetically and structurally by using thioflavin T (ThT) and transmission electron microscopy (TEM), respectively. LMW inhibitors were shown to have a differential impact on early-state aggregation. Insight provided here could direct future therapeutic design based on kinetic profiling of the process of fibril formation.
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Affiliation(s)
- Marie-Theres Hutchison
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Giovanni Bellomo
- Laboratory of Clinical Neurochemistry Department of Medicine and Surgery, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, Italy
| | - Alexey Cherepanov
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Elina Gurewitsch
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
| | - Moreno Lelli
- Chemistry Department, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM/CIRMMP), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Nina Morgner
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/Main, Germany
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10
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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: 12] [Impact Index Per Article: 6.0] [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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11
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Hjalte J, Hossain S, Hugerth A, Sjögren H, Wahlgren M, Larsson P, Lundberg D. Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated by 1H NMR and All-Atom Molecular Dynamics Simulations. Mol Pharm 2022; 19:904-917. [PMID: 35104408 PMCID: PMC8905580 DOI: 10.1021/acs.molpharmaceut.1c00883] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Understanding of peptide aggregation propensity is an important aspect in pharmaceutical development of peptide drugs. In this work, methodologies based on all-atom molecular dynamics (AA-MD) simulations and 1H NMR (in neat H2O) were evaluated as tools for identification and investigation of peptide aggregation. A series of structurally similar, pharmaceutically relevant peptides with known differences in aggregation behavior (D-Phe6-GnRH, ozarelix, cetrorelix, and degarelix) were investigated. The 1H NMR methodology was used to systematically investigate variations in aggregation with peptide concentration and time. Results show that 1H NMR can be used to detect the presence of coexisting classes of aggregates and the inclusion or exclusion of counterions in peptide aggregates. Interestingly, results suggest that the acetate counterions are included in aggregates of ozarelix and cetrorelix but not in aggregates of degarelix. The peptides investigated in AA-MD simulations (D-Phe6-GnRH, ozarelix, and cetrorelix) showed the same rank order of aggregation propensity as in the NMR experiments. The AA-MD simulations also provided molecular-level insights into aggregation dynamics, aggregation pathways, and the influence of different structural elements on peptide aggregation propensity and intermolecular interactions within the aggregates. Taken together, the findings from this study illustrate that 1H NMR and AA-MD simulations can be useful, complementary tools in early evaluation of aggregation propensity and formulation development for peptide drugs.
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Affiliation(s)
- Johanna Hjalte
- Food
Technology, Engineering and Nutrition, Lund
University, Box 124, 221 00 Lund, Sweden
| | - Shakhawath Hossain
- Department
of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Andreas Hugerth
- Ferring
Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Helen Sjögren
- Ferring
Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Marie Wahlgren
- Food
Technology, Engineering and Nutrition, Lund
University, Box 124, 221 00 Lund, Sweden
| | - Per Larsson
- Department
of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Dan Lundberg
- CR
Competence AB, Center for Chemistry and Chemical Engineering, Box 124, 221 00 Lund, Sweden
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12
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Sharma S, Modi P, Sharma G, Deep S. Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition. Biophys Chem 2021; 278:106665. [PMID: 34419715 DOI: 10.1016/j.bpc.2021.106665] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.
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Affiliation(s)
- Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Priya Modi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Gargi Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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13
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Sciaccaluga M, Megaro A, Bellomo G, Ruffolo G, Romoli M, Palma E, Costa C. An Unbalanced Synaptic Transmission: Cause or Consequence of the Amyloid Oligomers Neurotoxicity? Int J Mol Sci 2021; 22:ijms22115991. [PMID: 34206089 PMCID: PMC8199544 DOI: 10.3390/ijms22115991] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β (Aβ) 1-40 and 1-42 peptides are key mediators of synaptic and cognitive dysfunction in Alzheimer's disease (AD). Whereas in AD, Aβ is found to act as a pro-epileptogenic factor even before plaque formation, amyloid pathology has been detected among patients with epilepsy with increased risk of developing AD. Among Aβ aggregated species, soluble oligomers are suggested to be responsible for most of Aβ's toxic effects. Aβ oligomers exert extracellular and intracellular toxicity through different mechanisms, including interaction with membrane receptors and the formation of ion-permeable channels in cellular membranes. These damages, linked to an unbalance between excitatory and inhibitory neurotransmission, often result in neuronal hyperexcitability and neural circuit dysfunction, which in turn increase Aβ deposition and facilitate neurodegeneration, resulting in an Aβ-driven vicious loop. In this review, we summarize the most representative literature on the effects that oligomeric Aβ induces on synaptic dysfunction and network disorganization.
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Affiliation(s)
- Miriam Sciaccaluga
- Neurology Clinic, Department of Medicine and Surgery, University of Perugia, Santa Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.M.); (G.B.)
- Correspondence: (M.S.); (C.C.); Tel.: +39-0755858180 (M.S.); +39-0755784233 (C.C.)
| | - Alfredo Megaro
- Neurology Clinic, Department of Medicine and Surgery, University of Perugia, Santa Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.M.); (G.B.)
| | - Giovanni Bellomo
- Neurology Clinic, Department of Medicine and Surgery, University of Perugia, Santa Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.M.); (G.B.)
| | - Gabriele Ruffolo
- Department of Physiology and Pharmacology, Istituto Pasteur—Fondazione Cenci Bolognetti, University of Rome Sapienza, 00185 Rome, Italy; (G.R.); (E.P.)
- IRCCS San Raffaele Pisana, 00166 Rome, Italy
| | - Michele Romoli
- Neurology Unit, Rimini “Infermi” Hospital—AUSL Romagna, 47923 Rimini, Italy;
| | - Eleonora Palma
- Department of Physiology and Pharmacology, Istituto Pasteur—Fondazione Cenci Bolognetti, University of Rome Sapienza, 00185 Rome, Italy; (G.R.); (E.P.)
| | - Cinzia Costa
- Neurology Clinic, Department of Medicine and Surgery, University of Perugia, Santa Maria della Misericordia Hospital, 06132 Perugia, Italy; (A.M.); (G.B.)
- Correspondence: (M.S.); (C.C.); Tel.: +39-0755858180 (M.S.); +39-0755784233 (C.C.)
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14
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Sun Y, Kakinen A, Wan X, Moriarty N, Hunt CP, Li Y, Andrikopoulos N, Nandakumar A, Davis TP, Parish CL, Song Y, Ke PC, Ding F. Spontaneous Formation of β-sheet Nano-barrels during the Early Aggregation of Alzheimer's Amyloid Beta. NANO TODAY 2021; 38:101125. [PMID: 33936250 PMCID: PMC8081394 DOI: 10.1016/j.nantod.2021.101125] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Soluble low-molecular-weight oligomers formed during the early aggregation of amyloid peptides have been hypothesized as a major toxic species of amyloidogenesis. Herein, we performed the first synergic in silico, in vitro and in vivo validations of the structure, dynamics and toxicity of Aβ42 oligomers. Aβ peptides readily assembled into β-rich oligomers comprised of extended β-hairpins and β-strands. Nanosized β-barrels were observed with certainty with simulations, transmission electron microscopy and Fourier transform infrared spectroscopy, corroborated by immunohistochemistry, cell viability, apoptosis, inflammation, autophagy and animal behavior assays. Secondary and tertiary structural proprieties of these oligomers, such as the sequence regions with high β-sheet propensities and inter-residue contact frequency patterns, were similar to the properties known for Aβ fibrils. The unambiguous spontaneous formation of β-barrels in the early aggregation of Aβ42 supports their roles as the common toxic intermediates in Alzheimer's pathobiology and a target for Alzheimer's therapeutics.
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Affiliation(s)
- Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Xulin Wan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Food Science, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
| | - Niamh Moriarty
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Cameron P.J. Hunt
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Yuhuan Li
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, 200032, China
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas P. Davis
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Clare L. Parish
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville VIC 3052, Australia
| | - Yang Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Pu Chun Ke
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Address correspondence to: Yunxiang Sun: ; Yang Song: ; Pu Chun Ke: ; Feng Ding:
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15
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Son SH, Do JM, Yoo JN, Lee HW, Kim NK, Yoo HS, Gee MS, Kim JH, Seong JH, Inn KS, Seo MD, Lee JK, Kim NJ. Identification of ortho catechol-containing isoflavone as a privileged scaffold that directly prevents the aggregation of both amyloid β plaques and tau-mediated neurofibrillary tangles and its in vivo evaluation. Bioorg Chem 2021; 113:105022. [PMID: 34098397 DOI: 10.1016/j.bioorg.2021.105022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/03/2021] [Accepted: 05/23/2021] [Indexed: 12/15/2022]
Abstract
In this study, polyhydroxyisoflavones that directly prevent the aggregation of both amyloid β (Aβ) and tau were expediently synthesized via divergent Pd(0)-catalyzed Suzuki-Miyaura coupling and then biologically evaluated. By preliminary structure-activity relationship studies using thioflavin T (ThT) assays, an ortho-catechol containing isoflavone scaffold was proven to be crucial for preventing both Aβ aggregation and tau-mediated neurofibrillary tangle formation. Additional TEM experiment confirmed that ortho-catechol containing isoflavone 4d significantly prevented the aggregation of both Aβ and tau. To investigate the mode of action (MOA) of 4d, which possesses an ortho-catechol moiety, 1H-15N HSQC NMR analysis was thoroughly performed and the result indicated that 4d could directly inhibit both the formation of Aβ42 fibrils and the formation of tau-derived neurofibrils, probably through the catechol-mediated nucleation of tau. Finally, 4d was demonstrated to alleviate cognitive impairment and pathologies related to Alzheimer's disease in a 5XFAD transgenic mouse model.
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Affiliation(s)
- Seung Hwan Son
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ji Min Do
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ji-Na Yoo
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon 16499, Republic of Korea; Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Hyun Woo Lee
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Nam Kwon Kim
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyung-Seok Yoo
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Min Sung Gee
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jong-Ho Kim
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Ji Hye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Kyung-Soo Inn
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Min-Duk Seo
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon 16499, Republic of Korea; Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea.
| | - Jong Kil Lee
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea.
| | - Nam-Jung Kim
- College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea; Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Republic of Korea.
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16
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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17
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Wang Y, Xue Y, Wang S, Huang J, Yang X. Real-Time Analysis of Specific Binding between Apolipoprotein E Isoforms and Amyloid β-Peptide by Dual Polarization Interferometry. Anal Chem 2021; 93:1472-1479. [PMID: 33342209 DOI: 10.1021/acs.analchem.0c03542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
One of the pathogenesis hypotheses of Alzheimer's disease (AD) is amyloid depositions and neurofibrillary tangles. Apolipoprotein E (Apo E) acts a vital part in the development of AD by affecting the aggregation and clearance of amyloid-β (Aβ). In this paper, a dual polarization interferometry (DPI) technique was employed for a real-time investigation toward the binding events of Apo E isoforms, for instance, Apo E2, Apo E3, and Apo E4, with Aβ1-40. By evaluation of detailed binding information provided by DPI, the affinities between Apo E isoforms and Aβ1-40 follow the order of E4 > E3 > E2, and the dissociation constants (KD) of Aβ1-40 with Apo E2, Apo E3, and Apo E4 were determined to be 251 ± 37, 40 ± 0.65, and 24.6 ± 2.42 nM, respectively. Our findings reveal the isoform-specific binding behaviors from a kinetics perspective, which can help us understand that Apo E4 has a higher risk of causing AD because of its promoting effect on Aβ aggregation and fibrillation and inefficient clearance of Aβ. Remarkably, this work provides a promising method for exploring the dynamics of interactions between biomolecules and expectantly contributes to the development of AD drugs and therapies targeting Apo E and Aβ.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yu Xue
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
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18
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Leite JP, Gimeno A, Taboada P, Jiménez-Barbero JJ, Gales L. Dissection of the key steps of amyloid-β peptide 1-40 fibrillogenesis. Int J Biol Macromol 2020; 164:2240-2246. [PMID: 32771514 DOI: 10.1016/j.ijbiomac.2020.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 11/27/2022]
Abstract
The aggregation kinetics of Aβ1-40 peptide was characterized using a synergistic approach by a combination of nuclear magnetic resonance, thioflavin-T fluorescence, transmission electron microscopy and dynamic light scattering. A major finding is the experimental detection of high molecular weight oligomers (HMWO) that converts into fibrils nuclei. Our observations are consistent with a mechanism of Aβ1-40 fibrillogenesis that includes the following key steps: i) slow formation of HMWO (Rh ~ 20 nm); ii) conversion of the HMWO into more compact Rh ~ 10 nm fibrils nuclei; iii) fast formation of additional fibrils nuclei through fibril surface catalysed processes; and iv) growth of fibrils by addition of soluble Aβ species. Moreover, NMR diffusion experiments show that at 37 °C soluble Aβ1-40 remains intrinsically disordered and mostly in monomeric form despite evidences of the presence of dimers and/or other small oligomers. A mathematical model is proposed to simulate the aggregation kinetics of Aβ1-40.
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Affiliation(s)
- José P Leite
- i3S - Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Rua Alfredo Allen, 208, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira 228, Porto, Portugal
| | - Ana Gimeno
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
| | - Pablo Taboada
- Colloids and Polymers Physics Group, Particle Physics Department, 15782 Campus Vida, Universidade de Santiago de Compostela, Spain
| | - Jesús J Jiménez-Barbero
- CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain; Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain; Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - Luís Gales
- i3S - Instituto de Investigação e Inovação em Saúde, Rua Alfredo Allen, 208, Porto, Portugal; IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Rua Alfredo Allen, 208, Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Rua de Jorge Viterbo Ferreira 228, Porto, Portugal.
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19
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Koder Hamid M, Rüter A, Kuczera S, Olsson U. Slow Dissolution Kinetics of Model Peptide Fibrils. Int J Mol Sci 2020; 21:ijms21207671. [PMID: 33081320 PMCID: PMC7590008 DOI: 10.3390/ijms21207671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 11/25/2022] Open
Abstract
Understanding the kinetics of peptide self-assembly is important because of the involvement of peptide amyloid fibrils in several neurodegenerative diseases. In this paper, we have studied the dissolution kinetics of self-assembled model peptide fibrils after a dilution quench. Due to the low concentrations involved, the experimental method of choice was isothermal titration calorimetry (ITC). We show that the dissolution is a strikingly slow and reaction-limited process, that can be timescale separated from other rapid processes associated with dilution in the ITC experiment. We argue that the rate-limiting step of dissolution involves the breaking up of inter-peptide β–sheet hydrogen bonds, replacing them with peptide–water hydrogen bonds. Complementary pH experiments revealed that the self-assembly involves partial deprotonation of the peptide molecules.
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20
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Bellomo G, Cataldi S, Paciotti S, Paolini Paoletti F, Chiasserini D, Parnetti L. Measurement of CSF core Alzheimer disease biomarkers for routine clinical diagnosis: do fresh vs frozen samples differ? ALZHEIMERS RESEARCH & THERAPY 2020; 12:121. [PMID: 32993776 PMCID: PMC7526419 DOI: 10.1186/s13195-020-00689-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022]
Abstract
Background Cerebrospinal fluid (CSF) amyloid-beta (Aβ) 42/40 ratio, threonine-181-phosphorylated-tau (p-tau), and total-tau (t-tau) represent core biomarkers of Alzheimer disease (AD). The recent availability of automated platforms has represented a significant achievement for reducing the pre-analytical variability of these determinations in clinical setting. With respect to classical manual ELISAs, these platforms give us also the possibility to measure any single sample and to get the result within approximately 30 min. So far, reference values have been calculated from measurements obtained in frozen samples. In this work, we wanted to check if the values obtained in fresh CSF samples differ from those obtained in frozen samples, since this issue is mandatory in routine diagnostic work. Methods Fifty-eight consecutive CSF samples have been analyzed immediately after lumbar puncture and after 1-month deep freezing (− 80 °C). As an automated platform, we used Lumipulse G600-II (Fujirebio Inc.). Both the fresh and the frozen aliquots were analyzed in their storage tubes. Results In fresh samples, a mean increase of Aβ40 (6%), Aβ42 (2%), p-tau (2%), and t-tau (4%) was observed as compared to frozen samples, whereas a slight decrease was observed for Aβ42/Aβ40 ratio (4%), due to the higher deviation of Aβ40 in fresh samples compared to Aβ42. These differences are significant for Aβ40, Aβ42/Aβ40 ratio, p-tau, and t-tau. Nevertheless, the Aβ42/Aβ40 ratio showed a lower variability (smaller standard deviation of relative differences) with respect to Aβ42. With respect to the AD profile according to the A/T/(N) criteria for AD diagnosis, no significant changes in classification were observed when comparing results obtained in fresh vs frozen samples. Conclusions Small but significant differences have been found for Aβ40, Aβ42/Aβ40 ratio, p-tau, and t-tau in fresh vs frozen samples. Importantly, these differences did not imply a modification in the A/T/(N) classification system. In order to know if different cutoffs for fresh and frozen samples are required, larger, multi-center investigations are needed.
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Affiliation(s)
- Giovanni Bellomo
- Laboratory of Clinical Neurochemistry, Section of Neurology, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, PG, Italy
| | - Samuela Cataldi
- Laboratory of Clinical Neurochemistry, Section of Neurology, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, PG, Italy
| | - Silvia Paciotti
- Laboratory of Clinical Neurochemistry, Section of Neurology, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, PG, Italy.,Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, Piazza Lucio Severi 1/8, 06132, Perugia, PG, Italy
| | | | - Davide Chiasserini
- Department of Experimental Medicine, Section of Physiology and Biochemistry, University of Perugia, Piazza Lucio Severi 1/8, 06132, Perugia, PG, Italy
| | - Lucilla Parnetti
- Laboratory of Clinical Neurochemistry, Section of Neurology, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, PG, Italy. .,Section of Neurology, University of Perugia, Piazzale Lucio Severi 1/8, 06132, Perugia, PG, Italy.
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21
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Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chem Sci 2020; 11:6236-6247. [PMID: 32953019 PMCID: PMC7480182 DOI: 10.1039/c9sc06501f] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation.
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Affiliation(s)
- Alexander J Dear
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Anđela Šarić
- Department of Physics and Astronomy , Institute for the Physics of Living Systems , University College London , Gower Street , London WC1E 6BT , UK
- MRC Laboratory for Molecular Cell Biology , University College London , Gower St, WC1E 6BT , London , UK
| | - Thomas C T Michaels
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , MA 02138 , USA
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics , Aarhus University , Høegh-Guldbergs Gade 6B , DK-8000 Aarhus C , Denmark
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Cavendish Laboratory , Department of Physics , University of Cambridge , J J Thomson Avenue , Cambridge CB3 0HE , UK .
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22
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Sahoo BR, Cox SJ, Ramamoorthy A. High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease. Chem Commun (Camb) 2020; 56:4627-4639. [PMID: 32300761 PMCID: PMC7254607 DOI: 10.1039/d0cc01551b] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna in establishing the structure to function relationship for Aβ oligomers prevents the development of an effective treatment for AD. While the transient and heterogeneous properties of Aβ oligomers impose many challenges for structural investigation, an effective use of a combination of NMR techniques has successfully identified and characterized them at atomic-resolution. Here, we review the successful utilization of solution and solid-state NMR techniques to probe the aggregation and structures of small and large oligomers of Aβ. Biophysical studies utilizing the commonly used solution and 19F based NMR experiments to identify the formation of small size early intermediates and to obtain their structures, and dock-lock mechanism of fiber growth at atomic-resolution are discussed. In addition, the use of proton-detected magic angle spinning (MAS) solid-state NMR experiments to obtain high-resolution insights into the aggregation pathways and structures of large oligomers and other aggregates is also presented. We expect these NMR based studies to be valuable for real-time monitoring of the depletion of monomers and the formation of toxic oligomers and high-order aggregates under a variety of conditions, and to solve the high-resolution structures of small and large size oligomers for most amyloid proteins, and therefore to develop inhibitors and drugs.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics Program, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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23
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Yu HJ, Zhao W, Xie M, Li X, Sun M, He J, Wang L, Yu L. Real-Time Monitoring of Self-Aggregation of β-Amyloid by a Fluorescent Probe Based on Ruthenium Complex. Anal Chem 2020; 92:2953-2960. [PMID: 31941275 DOI: 10.1021/acs.analchem.9b03566] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Self-accumulation of amyloid-β protein (Aβ) into insoluble fibrils is the major hallmark of Alzheimer's disease. Real-time monitoring of fibril growth is essential for clarifying the mechanism underlying aggregation and discovering therapeutic targets. A variety of approaches including NMR, electron microscopy (EM), atomic force microscopy (AFM), and total internal reflection fluorescence microscopy (TIRFM) have been explored to monitor the fibril growth or reveal morphology of Aβ aggregates. However, none of the methods allow real-time observation under physiological conditions while without any perturbations. Here, we present a fluorescent probe [Ru(phen)2(fipc)]2+ (Ru-fipc) (phen = 1,10-phenanthroline, fipc = 5-fluoro-N-(1,10-phenanthrolin-5-yl)-1H-indole-2-carboxamide) that can bind to all the Aβ forms, i.e., monomers, oligomers, and fibrils, while not perturbing aggregation. Using this probe in combination with laser confocal microscopy, the entire aggregation process could be clearly and exactly imaged at the single fibril level. The reliability of Ru-fipc was confirmed based on colocalization with thioflavin T (ThT). Importantly, Ru-fipc can be used to monitor the very early nucleation and oligomerization process, which is thought to be a critical step in the development of neurotoxicity while it cannot be visualized with ThT. To our knowledge, this is the first fluorescent probe developed for real-time monitoring of Aβ aggregation, especially for the very early assembly stage, in solution with minimal perturbation. This method is suitable for in vitro and in vivo studies. We believe this would provide a valuable complementary tool for the study of pathogenesis and discovery of therapeutic targets of neurodegenerative diseases.
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Affiliation(s)
- Hui-Juan Yu
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Wei Zhao
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Mengting Xie
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Xiaoqing Li
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Ming Sun
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Jun He
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
| | - Lu Wang
- Department of Nuclear Medicine and PET/CT-MRI Center, The First Affiliated Hospital of Jinan University and Institute of Molecular and Functional Imaging , Jinan University , 613 West Huangpu Avenue , Guangzhou 510630 PR China
| | - Lin Yu
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , PR China
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24
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Cerofolini L, Ravera E, Bologna S, Wiglenda T, Böddrich A, Purfürst B, Benilova I, Korsak M, Gallo G, Rizzo D, Gonnelli L, Fragai M, De Strooper B, Wanker EE, Luchinat C. Mixing Aβ(1–40) and Aβ(1–42) peptides generates unique amyloid fibrils. Chem Commun (Camb) 2020; 56:8830-8833. [DOI: 10.1039/d0cc02463e] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solid-state NMR experiments reveal that the two isoforms of the beta-amyloid peptide (Aβ(1–40) and Aβ(1–42)) are able to form unique interlaced mixed fibrils.
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25
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Donnarumma F, Leone S, Delfi M, Emendato A, Ami D, Laurents DV, Natalello A, Spadaccini R, Picone D. Probing structural changes during amyloid aggregation of the sweet protein MNEI. FEBS J 2019; 287:2808-2822. [DOI: 10.1111/febs.15168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/20/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Federica Donnarumma
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Serena Leone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Masoud Delfi
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Alessandro Emendato
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Douglas V. Laurents
- Institute of Physical Chemistry ‘Rocasolano’ Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Antonino Natalello
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Roberta Spadaccini
- Department of Science and Technology Università degli Studi del Sannio Benevento Italy
| | - Delia Picone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
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26
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Tomaselli S, La Vitola P, Pagano K, Brandi E, Santamaria G, Galante D, D’Arrigo C, Moni L, Lambruschini C, Banfi L, Lucchetti J, Fracasso C, Molinari H, Forloni G, Balducci C, Ragona L. Biophysical and in Vivo Studies Identify a New Natural-Based Polyphenol, Counteracting Aβ Oligomerization in Vitro and Aβ Oligomer-Mediated Memory Impairment and Neuroinflammation in an Acute Mouse Model of Alzheimer's Disease. ACS Chem Neurosci 2019; 10:4462-4475. [PMID: 31603646 DOI: 10.1021/acschemneuro.9b00241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In this study natural-based complex polyphenols, obtained through a smart synthetic approach, have been evaluated for their ability to inhibit the formation of Aβ42 oligomers, the most toxic species causing synaptic dysfunction, neuroinflammation, and neuronal death leading to the onset and progression of Alzheimer's disease. In vitro neurotoxicity tests on primary hippocampal neurons have been employed to select nontoxic candidates. Solution NMR and molecular docking studies have been performed to clarify the interaction mechanism of Aβ42 with the synthesized polyphenol derivatives, and highlight the sterical and chemical requirements important for their antiaggregating activity. NMR results indicated that the selected polyphenolic compounds target Aβ42 oligomeric species. Combined NMR and docking studies indicated that the Aβ42 central hydrophobic core, namely, the 17-31 region, is the main interaction site. The length of the peptidomimetic scaffold and the presence of a guaiacol moiety were identified as important requirements for the antiaggregating activity. In vivo experiments on an Aβ42 oligomer-induced acute mouse model highlighted that the most promising polyphenolic derivative (PP04) inhibits detrimental effects of Aβ42 oligomers on memory and glial cell activation. NMR kinetic studies showed that PP04 is endowed with the chemical features of true inhibitors, strongly affecting both the Aβ42 nucleation and growth rates, thus representing a promising candidate to be further developed into an effective drug against neurodegenerative diseases of the amyloid type.
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Affiliation(s)
- Simona Tomaselli
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Milan 20133, Italy
| | - Pietro La Vitola
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan 20156, Italy
| | - Katiuscia Pagano
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Milan 20133, Italy
| | - Edoardo Brandi
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan 20156, Italy
| | - Giulia Santamaria
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan 20156, Italy
| | - Denise Galante
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Genoa 16149, Italy
| | - Cristina D’Arrigo
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Genoa 16149, Italy
| | - Lisa Moni
- Department of Chemistry and Industrial Chemistry, Università di Genova, Genova 16146, Italy
| | - Chiara Lambruschini
- Department of Chemistry and Industrial Chemistry, Università di Genova, Genova 16146, Italy
| | - Luca Banfi
- Department of Chemistry and Industrial Chemistry, Università di Genova, Genova 16146, Italy
| | - Jacopo Lucchetti
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan 20156, Italy
| | - Claudia Fracasso
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan 20156, Italy
| | - Henriette Molinari
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Milan 20133, Italy
| | - Gianluigi Forloni
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan 20156, Italy
| | - Claudia Balducci
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan 20156, Italy
| | - Laura Ragona
- Istituto per lo Studio delle Macromolecole (ISMAC), CNR, Milan 20133, Italy
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27
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Katyal N, Deep S. A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways. Phys Chem Chem Phys 2019; 21:24269-24285. [PMID: 31670327 DOI: 10.1039/c9cp03763b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, Delhi, India.
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28
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Rezaei-Ghaleh N, Parigi G, Zweckstetter M. Reorientational Dynamics of Amyloid-β from NMR Spin Relaxation and Molecular Simulation. J Phys Chem Lett 2019; 10:3369-3375. [PMID: 31181936 PMCID: PMC6598774 DOI: 10.1021/acs.jpclett.9b01050] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer's disease. As an intrinsically disordered protein, Aβ undergoes extensive dynamics on multiple length and time scales. Access to a comprehensive picture of the reorientational dynamics in Aβ requires therefore the combination of complementary techniques. Here, we integrate 15N spin relaxation rates at three magnetic fields with microseconds-long molecular dynamics simulation, ensemble-based hydrodynamic calculations, and previously published nanosecond fluorescence correlation spectroscopy to investigate the reorientational dynamics of Aβ1-40 (Aβ40) at single-residue resolution. The integrative analysis shows that librational and dihedral angle fluctuations occurring at fast and intermediate time scales are not sufficient to decorrelate orientational memory in Aβ40. Instead, slow segmental motions occurring at ∼5 ns are detected throughout the Aβ40 sequence and reach up to ∼10 ns for selected residues. We propose that the modulation of time scales of reorientational dynamics with respect to intra- and intermolecular diffusion plays an important role in disease-related Aβ aggregation.
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Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Department
of Neurology, University Medical Center
Goettingen, 37075 Goettingen, Germany
- Department
for NMR-Based Structural Biology, Max Planck
Institute for Biophysical Chemistry, 37077 Goettingen, Germany
- E-mail:
| | - Giacomo Parigi
- Magnetic
Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Markus Zweckstetter
- Department
of Neurology, University Medical Center
Goettingen, 37075 Goettingen, Germany
- Department
for NMR-Based Structural Biology, Max Planck
Institute for Biophysical Chemistry, 37077 Goettingen, Germany
- Research
Group for Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Goettingen, Germany
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29
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Bellomo G, Bologna S, Cerofolini L, Paciotti S, Gatticchi L, Ravera E, Parnetti L, Fragai M, Luchinat C. Dissecting the Interactions between Human Serum Albumin and α-Synuclein: New Insights on the Factors Influencing α-Synuclein Aggregation in Biological Fluids. J Phys Chem B 2019; 123:4380-4386. [PMID: 31034772 DOI: 10.1021/acs.jpcb.9b02381] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
α-Synuclein (α-syn) is found to be naturally present in biofluids such as cerebrospinal fluid (CSF) and serum. Human serum albumin (HSA) is the most abundant protein found in these biofluids, which, beyond transporting hormones and drugs, also exerts a chaperone-like activity binding other proteins in blood and inhibiting their aggregation. Contrasting results are reported in the literature about the effects of albumin on α-syn aggregation. We characterized the binding region of HSA on α-syn by high-field solution NMR spectroscopy and the effect of HSA on α-syn aggregation by thioflavin-T (ThT) fluorescence under both low-ionic-strength and physiological conditions at the albumin concentration in serum and CSF. We found that HSA, at the concentration found in human serum, slows the aggregation of α-syn significantly. α-Syn interacts with HSA in an ionic strength- and pH-dependent manner. The binding is driven by hydrophobic interactions at the N-terminus under physiological experimental conditions and by electrostatic interactions at the C-terminus at low ionic strength. This work provides novel information about the proteostasis of α-syn in biofluids and supports the hypothesis of a chaperone-like behavior of HSA.
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Affiliation(s)
- Giovanni Bellomo
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Sara Bologna
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Silvia Paciotti
- Department of Experimental Medicine , University of Perugia , Piazzale Gambuli 1 , 06132 Perugia , Italy
| | - Leonardo Gatticchi
- Department of Experimental Medicine , University of Perugia , Piazzale Gambuli 1 , 06132 Perugia , Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Lucilla Parnetti
- Clinica Neurologica , Università degli Studi di Perugia , Piazzale Gambuli 1 , 06132 Perugia , Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) , University of Florence , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
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30
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Brender JR, Ghosh A, Kotler SA, Krishnamoorthy J, Bera S, Morris V, Sil TB, Garai K, Reif B, Bhunia A, Ramamoorthy A. Probing transient non-native states in amyloid beta fiber elongation by NMR. Chem Commun (Camb) 2019; 55:4483-4486. [PMID: 30917192 DOI: 10.1039/c9cc01067j] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Using NMR to probe transient binding of Aβ1-40 monomers to fibers, we find partially bound conformations with the highest degree of interaction near F19-K28 and a lesser degree of interaction near the C-terminus (L34-G37). This represents a shift away from the KLVFFA recognition sequence (residues 16-21) currently used for inhibitor design.
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