1
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Yang Q, Hosseini E, Yao P, Pütz S, Gelléri M, Bonn M, Parekh SH, Liu X. Self-Blinking Thioflavin T for Super-resolution Imaging. J Phys Chem Lett 2024; 15:7591-7596. [PMID: 39028951 PMCID: PMC11299178 DOI: 10.1021/acs.jpclett.4c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 07/04/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Thioflavin T (ThT) is a typical dye used to visualize the aggregation and formation of fibrillar structures, e.g., amyloid fibrils and peptide nanofibrils. ThT has been considered to produce stable fluorescence when interacting with aggregated proteins. For single-molecule localization microscopy (SMLM)-based optical super-resolution imaging, a photoswitching/blinking fluorescence property is required. Here we demonstrate that, in contrast to previous reports, ThT exhibits intrinsic stochastic blinking properties, without the need for blinking imaging buffer, in stable binding conditions. The blinking properties (photon number, blinking time, and on-off duty cycle) of ThT at the single-molecule level (for ultralow concentrations) were investigated under different conditions. As a proof of concept, we performed SMLM imaging of ThT-labeled α-synuclein fibrils measured in air and PBS buffer.
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Affiliation(s)
- Qiqi Yang
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Elnaz Hosseini
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Peigen Yao
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sabine Pütz
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Márton Gelléri
- Institute
of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany
| | - Mischa Bonn
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, University of
Texas at Austin, Austin, Texas 78712, United States
| | - Xiaomin Liu
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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2
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Rodina N, Hornung S, Sarkar R, Suladze S, Peters C, Schmid PWN, Niu Z, Haslbeck M, Buchner J, Kapurniotu A, Reif B. Modulation of Alzheimer's Disease Aβ40 Fibril Polymorphism by the Small Heat Shock Protein αB-Crystallin. J Am Chem Soc 2024; 146:19077-19087. [PMID: 38973199 PMCID: PMC11258688 DOI: 10.1021/jacs.4c03504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/09/2024]
Abstract
Deposition of amyloid plaques in the brains of Alzheimer's disease (AD) patients is a hallmark of the disease. AD plaques consist primarily of the beta-amyloid (Aβ) peptide but can contain other factors such as lipids, proteoglycans, and chaperones. So far, it is unclear how the cellular environment modulates fibril polymorphism and how differences in fibril structure affect cell viability. The small heat-shock protein (sHSP) alpha-B-Crystallin (αBC) is abundant in brains of AD patients, and colocalizes with Aβ amyloid plaques. Using solid-state NMR spectroscopy, we show that the Aβ40 fibril seed structure is not replicated in the presence of the sHSP. αBC prevents the generation of a compact fibril structure and leads to the formation of a new polymorph with a dynamic N-terminus. We find that the N-terminal fuzzy coat and the stability of the C-terminal residues in the Aβ40 fibril core affect the chemical and thermodynamic stability of the fibrils and influence their seeding capacity. We believe that our results yield a better understanding of how sHSP, such as αBC, that are part of the cellular environment, can affect fibril structures related to cell degeneration in amyloid diseases.
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Affiliation(s)
- Natalia Rodina
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Simon Hornung
- Division
of Peptide Biochemistry, TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 5, Freising 85354, Germany
| | - Riddhiman Sarkar
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Saba Suladze
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Carsten Peters
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Philipp W. N. Schmid
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Zheng Niu
- School
of Pharmacy, Henan University, Kaifeng, Henan 475004, China
| | - Martin Haslbeck
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Johannes Buchner
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
| | - Aphrodite Kapurniotu
- Division
of Peptide Biochemistry, TUM School of Life Sciences, Technical University of Munich, Emil-Erlenmeyer-Forum 5, Freising 85354, Germany
| | - Bernd Reif
- Bayerisches
NMR Zentrum (BNMRZ) at the Department of Biosciences,
School of Natural SciencesCenter for Functional Protein Assemblies
(CPA), Department of Biosciences, Technische
Universität München, Lichtenbergstr. 4, Garching 85747, Germany
- Helmholtz-Zentrum
München (HMGU), Deutsches Forschungszentrum für Gesundheit
und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, Neuherberg 85764, Germany
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3
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Rusakov K, El-Turabi A, Reimer L, Jensen PH, Hanczyc P. Thioflavin T─a Reporter of Microviscosity in Protein Aggregation Process: The Study Case of α-Synuclein. J Phys Chem Lett 2024; 15:6685-6690. [PMID: 38899873 PMCID: PMC11215780 DOI: 10.1021/acs.jpclett.4c00699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024]
Abstract
Thioflavin T (ThT) informed microviscosity changes can be used to monitor protein aggregation. Steady-state, time-resolved and lasing spectroscopy were used to detect transient states in α-synuclein - a protein associated with Parkinson's disease. The major focus was on the nucleation phase, where conventional ThT fluorescence assay lacks appropriate sensitivity to detect early stage oligomers. Instead, lasing spectroscopy and lasing threshold parameters, in particular, were sensitive to detecting protein oligomers. Through lasing spectroscopy, a change in microviscosity correlating with the stages of protein aggregation was observed at two wavelengths 405 and 440 nm. The two wavelengths are associated with free dye molecules and β-sheet bound ThT molecules. This provides a perspective on elucidating the early formed protein aggregation, a critical aspect in understanding the pathogenesis of neurodegenerative diseases. The insights from the presented study shows the potential of using lasing spectroscopy as a sensitive tool in studying protein aggregation dynamics.
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Affiliation(s)
- Konstantin Rusakov
- Faculty
of Construction and Environmental Engineering, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Aadil El-Turabi
- University
of Oxford, Jenner Institute, Nuffield Department
of Medicine, OX3 7DQ Oxford, U.K.
| | - Lasse Reimer
- DANDRITE,
Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Poul Henning Jensen
- DANDRITE,
Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Piotr Hanczyc
- Institute
of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
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4
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Anselmo S, Sancataldo G, Vetri V. Deciphering amyloid fibril molecular maturation through FLIM-phasor analysis of thioflavin T. BIOPHYSICAL REPORTS 2024; 4:100145. [PMID: 38404533 PMCID: PMC10884809 DOI: 10.1016/j.bpr.2024.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024]
Abstract
The investigation of amyloid fibril formation is paramount for advancing our understanding of neurodegenerative diseases and for exploring potential correlated therapeutic strategies. Moreover, the self-assembling properties of amyloid fibrils show promise for the development of advanced protein-based biomaterials. Among the methods employed to monitor protein aggregation processes, fluorescence has emerged as a powerful tool. Its exceptional sensitivity enables the detection of early-stage aggregation events that are otherwise challenging to observe. This research underscores the pivotal role of fluorescence analysis, particularly in investigating the aggregation processes of hen egg white lysozyme, a model protein extensively studied for insights into amyloid fibril formation. By combining classical spectroscopies with fluorescence microscopy and by exploiting the fluorescence properties (intensity and lifetime) of the thioflavin T, we were able to noninvasively monitor key and complex molecular aspects of the process. Intriguingly, the fluorescence lifetime imaging-phasor analysis of thioflavin T fluorescence lifetime on structures at different stages of aggregation allowed to decipher the complex fluorescence decay behavior, highlighting that their changes rise from the combination of specific binding to amyloid typical cross-β structures and of the rigidity of the molecular environment.
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Affiliation(s)
- Sara Anselmo
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
| | - Giuseppe Sancataldo
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
| | - Valeria Vetri
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
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5
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Sulatsky MI, Stepanenko OV, Stepanenko OV, Kuznetsova IM, Turoverov KK, Sulatskaya AI. Prediction of the Feasibility of Using the ≪Gold Standard≫ Thioflavin T to Detect Amyloid Fibril in Acidic Media. Anal Chem 2024; 96:2158-2164. [PMID: 38269442 DOI: 10.1021/acs.analchem.3c05118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Ordered protein aggregates, amyloid fibrils, form toxic plaques in the human body in amyloidosis and neurodegenerative diseases and provide adaptive benefits to pathogens and to reduce the nutritional value of legumes. To identify the amyloidogenic properties of proteins and study the processes of amyloid fibril formation and degradation, the cationic dye thioflavin T (ThT) is the most commonly used. However, its use in acidic environments that induce amyloid formation in vitro can sometimes lead to misinterpretation of experimental results due to electrostatic repulsion. In this work, we show that calculating the net charge per residue of amyloidogenic proteins or peptides is a simple and effective approach for predicting whether their fibrils will interact with ThT at acidic pH. In particular, it was shown that at pH 2, proteins and peptides with a net charge per residue > +0.18 are virtually unstained by this fluorescent probe. The applicability of the proposed approach was demonstrated by predicting and experimentally confirming the absence of ThT interaction with amyloids formed from green fluorescent (sfGFP) and odorant-binding (bOBP) proteins, whose fibrillogenesis was first carried out in an acidic environment. Correct experimental evidence that the inability to detect these fibrils under acidic conditions is precisely because of the lack of dye binding to amyloids (and not their specific structure or the low fluorescence quantum yield of the bound dye) and that the number of ThT molecules associated with fibrils increases with decreasing acidity of the medium was obtained by using the equilibrium microdialysis approach.
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Affiliation(s)
- Maksim I Sulatsky
- Laboratory of cell morphology, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Olesya V Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Olga V Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Anna I Sulatskaya
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
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6
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Khan S, Naeem A. Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity. J Biomol Struct Dyn 2024; 42:346-361. [PMID: 36974939 DOI: 10.1080/07391102.2023.2192802] [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: 02/03/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Abstract
This study investigates the ability of bovine serum albumin (BSA) to act as an extracellular chaperone (EC) on human hemoglobin (Hb) at a pH of 7.4. The best temperature for studying this behavior was determined by analyzing Hb's aggregation kinetics at multiple temperatures. 55 °C was chosen as the optimal temperature for forming Hb amyloids. BSA was then tested at various concentrations (20-100 μM) to assess its chaperone-like activity on Hb at 55 °C. At a concentration of 100 μM, BSA exhibits chaperone-like activity with a client protein:BSA ratio of 1:10. The high ratio implies that the chaperone activity of BSA is favored by the effects of macromolecular crowding. The results showed that BSA has the potential to inhibit Hb's dissociation into alpha and beta subunits and protein aggregation by inhibiting secondary nucleation. BSA also causes the depolymerization of fibrils over time. The results were validated using molecular docking and all-atom molecular dynamics simulations. MD analysis such as RMSD, RMSF, Rg, SASA, Hydrogen bond, PCA, Free energy landscape (FEL) revealed that the stability of hemoglobin is greater when it is bound to BSA compared to unbound state. The study suggests that BSA can potentially bind to Hb dimers and reduce excitonic interactions, which reduces Hb aggregation. These results are consistent with the aggregation kinetics experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sadaf Khan
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Aabgeena Naeem
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
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7
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Stepanenko OV, Sulatskaya AI, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV. Mammalian odorant-binding proteins are prone to form amorphous aggregates and amyloid fibrils. Int J Biol Macromol 2023; 253:126872. [PMID: 37722633 DOI: 10.1016/j.ijbiomac.2023.126872] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023]
Abstract
Odorant-binding proteins are involved in perceiving smell by capturing odorants within the protein's β-barrel. On the example of bovine odorant-binding protein (bOBP), the structural organization of such proteins and their ability to bind ligands under various conditions in vitro were examined. We found a tendency of bOBP to form oligomers and small amorphous aggregates without disturbing the integrity of protein monomers at physiological conditions. Changes in environmental parameters (increased temperature and pH) favored the formation of larger and dense supramolecular complexes that significantly reduce the binding of ligands by bOBP. The ability of bOBP to form fibrillar aggregates with the properties of amyloids, including high cytotoxicity, was revealed at sample stirring (even at physiological temperature and pH), at medium acidification or pre-solubilization with hexafluoroisopropanol. Fibrillogenesis of bOBP was initiated by the dissociation of the protein's supramolecular complexes into monomers and the destabilization of the protein's β-barrels without a significant destruction of its native β-strands.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia.
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, 4 Tikhoretsky ave, 194064 St. Petersburg, Russia.
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8
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Bigi A, Cascella R, Cecchi C. α-Synuclein oligomers and fibrils: partners in crime in synucleinopathies. Neural Regen Res 2023; 18:2332-2342. [PMID: 37282450 PMCID: PMC10360081 DOI: 10.4103/1673-5374.371345] [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] [Indexed: 06/08/2023] Open
Abstract
The misfolding and aggregation of α-synuclein is the general hallmark of a group of devastating neurodegenerative pathologies referred to as synucleinopathies, such as Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. In such conditions, a range of different misfolded aggregates, including oligomers, protofibrils, and fibrils, are present both in neurons and glial cells. Growing experimental evidence supports the proposition that soluble oligomeric assemblies, formed during the early phases of the aggregation process, are the major culprits of neuronal toxicity; at the same time, fibrillar conformers appear to be the most efficient at propagating among interconnected neurons, thus contributing to the spreading of α-synuclein pathology. Moreover, α-synuclein fibrils have been recently reported to release soluble and highly toxic oligomeric species, responsible for an immediate dysfunction in the recipient neurons. In this review, we discuss the current knowledge about the plethora of mechanisms of cellular dysfunction caused by α-synuclein oligomers and fibrils, both contributing to neurodegeneration in synucleinopathies.
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Affiliation(s)
- Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, Florence, Italy
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9
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Belousov MV, Kosolapova AO, Fayoud H, Sulatsky MI, Sulatskaya AI, Romanenko MN, Bobylev AG, Antonets KS, Nizhnikov AA. OmpC and OmpF Outer Membrane Proteins of Escherichia coli and Salmonella enterica Form Bona Fide Amyloids. Int J Mol Sci 2023; 24:15522. [PMID: 37958507 PMCID: PMC10649029 DOI: 10.3390/ijms242115522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Outer membrane proteins (Omps) of Gram-negative bacteria represent porins involved in a wide range of virulence- and pathogenesis-related cellular processes, including transport, adhesion, penetration, and the colonization of host tissues. Most outer membrane porins share a specific spatial structure called the β-barrel that provides their structural integrity within the membrane lipid bilayer. Recent data suggest that outer membrane proteins from several bacterial species are able to adopt the amyloid state alternative to their β-barrel structure. Amyloids are protein fibrils with a specific spatial structure called the cross-β that gives them an unusual resistance to different physicochemical influences. Various bacterial amyloids are known to be involved in host-pathogen and host-symbiont interactions and contribute to colonization of host tissues. Such an ability of outer membrane porins to adopt amyloid state might represent an important mechanism of bacterial virulence. In this work, we investigated the amyloid properties of the OmpC and OmpF porins from two species belonging to Enterobacteriaceae family, Escherichia coli, and Salmonella enterica. We demonstrated that OmpC and OmpF of E. coli and S. enterica form toxic fibrillar aggregates in vitro. These aggregates exhibit birefringence upon binding Congo Red dye and show characteristic reflections under X-ray diffraction. Thus, we confirmed amyloid properties for OmpC of E. coli and demonstrated bona fide amyloid properties for three novel proteins: OmpC of S. enterica and OmpF of E. coli and S. enterica in vitro. All four studied porins were shown to form amyloid fibrils at the surface of E. coli cells in the curli-dependent amyloid generator system. Moreover, we found that overexpression of recombinant OmpC and OmpF in the E. coli BL21 strain leads to the formation of detergent- and protease-resistant amyloid-like aggregates and enhances the birefringence of bacterial cultures stained with Congo Red. We also detected detergent- and protease-resistant aggregates comprising OmpC and OmpF in S. enterica culture. These data are important in the context of understanding the structural dualism of Omps and its relation to pathogenesis.
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Affiliation(s)
- Mikhail V. Belousov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (H.F.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anastasiia O. Kosolapova
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (H.F.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Haidar Fayoud
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (H.F.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (M.I.S.); (A.I.S.)
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (M.I.S.); (A.I.S.)
| | - Maria N. Romanenko
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (H.F.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Kirill S. Antonets
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (H.F.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (H.F.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
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10
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MacKeigan TP, Morgan ML, Stys PK. Quantitation of Tissue Amyloid via Fluorescence Spectroscopy Using Controlled Concentrations of Thioflavin-S. Molecules 2023; 28:molecules28114483. [PMID: 37298959 DOI: 10.3390/molecules28114483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Amyloids are misfolded proteins that aggregate into fibrillar structures, the accumulation of which is associated with the pathogenesis of many neurodegenerative diseases, such as Alzheimer's disease (AD). Early, sensitive detection of these misfolded aggregates is of great interest to the field, as amyloid deposition begins well before the presentation of clinical symptoms. Thioflavin-S (ThS) is a fluorescent probe commonly used to detect amyloid pathology. Protocols for ThS staining vary, but they often use high staining concentrations followed by differentiation, which causes varying levels of non-specific staining and potentially leaves more subtle amyloid deposition unidentified. In this study, we developed an optimized ThS staining protocol for the sensitive detection of β-amyloids in the widely used 5xFAD Alzheimer's mouse model. Controlled dye concentrations together with fluorescence spectroscopy and advanced analytical methods enabled not only the visualization of plaque pathology, but also the detection of subtle and widespread protein misfolding throughout the 5xFAD white matter and greater parenchyma. Together, these findings demonstrate the efficacy of a controlled ThS staining protocol and highlight the potential use of ThS for the detection of protein misfolding that precedes clinical manifestation of disease.
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Affiliation(s)
- Tatiana P MacKeigan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Megan L Morgan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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11
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Wang R, Pang SC, Li JY, Li CL, Liu JM, Wang YM, Chen ML, Li YB. A review of the current research on in vivo and in vitro detection for alpha-synuclein: a biomarker of Parkinson's disease. Anal Bioanal Chem 2023; 415:1589-1605. [PMID: 36688984 DOI: 10.1007/s00216-023-04520-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023]
Abstract
Parkinson's disease is a health-threatening neurodegenerative disease of the elderly with clinical manifestations of motor and non-motor deficits such as tremor palsy and loss of smell. Alpha-synuclein (α-Syn) is the pathological basis of PD, it can abnormally aggregate into insoluble forms such as oligomers, fibrils, and plaques, causing degeneration of nigrostriatal dopaminergic neurons in the substantia nigra in the patient's brain and the formation of Lewy bodies (LBs) and Lewy neuritis (LN) inclusions. As a result, achieving α-Syn aggregate detection in the early stages of PD can effectively stop or delay the progression of the disease. In this paper, we provide a brief overview and analysis of the molecular structures and α-Syn in vivo and in vitro detection methods, such as mass spectrometry, antigen-antibody recognition, electrochemical sensors, and imaging techniques, intending to provide more technological support for detecting α-Syn early in the disease and intervening in the progression of Parkinson's disease.
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Affiliation(s)
- Rui Wang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, China.,College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Shu-Chao Pang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, 300381, China
| | - Jing-Ya Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Chan-Lian Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Jun-Miao Liu
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Yu-Ming Wang
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Mei-Ling Chen
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Yu-Bo Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
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12
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Pancoe SX, Wang YJ, Shimogawa M, Perez RM, Giannakoulias S, Petersson EJ. Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation. J Mol Biol 2022; 434:167859. [PMID: 36270580 PMCID: PMC9922159 DOI: 10.1016/j.jmb.2022.167859] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Fibrillar aggregates of the α-synuclein (αS) protein are the hallmark of Parkinson's Disease and related neurodegenerative disorders. Characterization of the effects of mutations and post-translational modifications (PTMs) on the αS aggregation rate can provide insight into the mechanism of fibril formation, which remains elusive in spite of intense study. A comprehensive collection (375 examples) of mutant and PTM aggregation rate data measured using the fluorescent probe thioflavin T is presented, as well as a summary of the effects of fluorescent labeling on αS aggregation (20 examples). A curated set of 131 single mutant de novo aggregation experiments are normalized to wild type controls and analyzed in terms of structural data for the monomer and fibrillar forms of αS. These tabulated data serve as a resource to the community to help in interpretation of aggregation experiments and to potentially be used as inputs for computational models of aggregation.
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Affiliation(s)
- Samantha X Pancoe
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Marie Shimogawa
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Ryann M Perez
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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13
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Kachkin DV, Volkov KV, Sopova JV, Bobylev AG, Fedotov SA, Inge-Vechtomov SG, Galzitskaya OV, Chernoff YO, Rubel AA, Aksenova AY. Human RAD51 Protein Forms Amyloid-like Aggregates In Vitro. Int J Mol Sci 2022; 23:ijms231911657. [PMID: 36232958 PMCID: PMC9570251 DOI: 10.3390/ijms231911657] [Citation(s) in RCA: 1] [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: 08/24/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022] Open
Abstract
RAD51 is a central protein of homologous recombination and DNA repair processes that maintains genome stability and ensures the accurate repair of double-stranded breaks (DSBs). In this work, we assessed amyloid properties of RAD51 in vitro and in the bacterial curli-dependent amyloid generator (C-DAG) system. Resistance to ionic detergents, staining with amyloid-specific dyes, polarized microscopy, transmission electron microscopy (TEM), X-ray diffraction and other methods were used to evaluate the properties and structure of RAD51 aggregates. The purified human RAD51 protein formed detergent-resistant aggregates in vitro that had an unbranched cross-β fibrillar structure, which is typical for amyloids, and were stained with amyloid-specific dyes. Congo-red-stained RAD51 aggregates demonstrated birefringence under polarized light. RAD51 fibrils produced sharp circular X-ray reflections at 4.7 Å and 10 Å, demonstrating that they had a cross-β structure. Cytoplasmic aggregates of RAD51 were observed in cell cultures overexpressing RAD51. We demonstrated that a key protein that maintains genome stability, RAD51, has amyloid properties in vitro and in the C-DAG system and discussed the possible biological relevance of this observation.
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Affiliation(s)
- Daniel V. Kachkin
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill V. Volkov
- Research Resource Center “Molecular and Cell Technologies”, Research Park, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Julia V. Sopova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Center of Transgenesis and Genome Editing, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alexander G. Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
| | - Sergei A. Fedotov
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Sergei G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Oxana V. Galzitskaya
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 3 Institutskaya St., 142290 Moscow, Russia
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
| | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (A.A.R.); (A.Y.A.)
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14
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Sarkar D, Maity NC, Shome G, Varnava KG, Sarojini V, Vivekanandan S, Sahoo N, Kumar S, Mandal AK, Biswas R, Bhunia A. Mechanistic insight into functionally different human islet polypeptide (hIAPP) amyloid: the intrinsic role of the C-terminal structural motifs. Phys Chem Chem Phys 2022; 24:22250-22262. [PMID: 36098073 DOI: 10.1039/d2cp01650h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeting amyloidosis requires high-resolution insight into the underlying mechanisms of amyloid aggregation. The sequence-specific intrinsic properties of a peptide or protein largely govern the amyloidogenic propensity. Thus, it is essential to delineate the structural motifs that define the subsequent downstream amyloidogenic cascade of events. Additionally, it is important to understand the role played by extrinsic factors, such as temperature or sample agitation, in modulating the overall energy barrier that prompts divergent nucleation events. Consequently, these changes can affect the fibrillation kinetics, resulting in structurally and functionally distinct amyloidogenic conformers associated with disease pathogenesis. Here, we have focused on human Islet Polypeptide (hIAPP) amyloidogenesis for the full-length peptide along with its N- and C-terminal fragments, under different temperatures and sample agitation conditions. This helped us to gain a comprehensive understanding of the intrinsic role of specific functional epitopes in the primary structure of the peptide that regulates amyloidogenesis and subsequent cytotoxicity. Intriguingly, our study involving an array of biophysical experiments and ex vivo data suggests a direct influence of external changes on the C-terminal fibrillating sequence. Furthermore, the observations indicate a possible collaborative role of this segment in nucleating hIAPP amyloidogenesis in a physiological scenario, thus making it a potential target for future therapeutic interventions.
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Affiliation(s)
- Dibakar Sarkar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Narayan Chandra Maity
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Gourav Shome
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Kyriakos Gabriel Varnava
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | | | - Nirakar Sahoo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, Texas, 78539, USA
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Kolkata 700 091, India
| | - Ranjit Biswas
- Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Sector-III, Salt Lake, Kolkata 700106, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, EN 80, Sector V, Kolkata 700 091, India.
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15
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Structure-specific amyloid precipitation in biofluids. Nat Chem 2022; 14:1045-1053. [PMID: 35798951 DOI: 10.1038/s41557-022-00976-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/16/2022] [Indexed: 11/08/2022]
Abstract
The composition of soluble toxic protein aggregates formed in vivo is currently unknown in neurodegenerative diseases, due to their ultra-low concentration in human biofluids and their high degree of heterogeneity. Here we report a method to capture amyloid-containing aggregates in human biofluids in an unbiased way, a process we name amyloid precipitation. We use a structure-specific chemical dimer, a Y-shaped, bio-inspired small molecule with two capture groups, for amyloid precipitation to increase affinity. Our capture molecule for amyloid precipitation (CAP-1) consists of a derivative of Pittsburgh Compound B (dimer) to target the cross β-sheets of amyloids and a biotin moiety for surface immobilization. By coupling CAP-1 to magnetic beads, we demonstrate that we can target the amyloid structure of all protein aggregates present in human cerebrospinal fluid, isolate them for analysis and then characterize them using single-molecule fluorescence imaging and mass spectrometry. Amyloid precipitation enables unbiased determination of the molecular composition and structural features of the in vivo aggregates formed in neurodegenerative diseases.
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16
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Kell DB, Laubscher GJ, Pretorius E. A central role for amyloid fibrin microclots in long COVID/PASC: origins and therapeutic implications. Biochem J 2022; 479:537-559. [PMID: 35195253 PMCID: PMC8883497 DOI: 10.1042/bcj20220016] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
Post-acute sequelae of COVID (PASC), usually referred to as 'Long COVID' (a phenotype of COVID-19), is a relatively frequent consequence of SARS-CoV-2 infection, in which symptoms such as breathlessness, fatigue, 'brain fog', tissue damage, inflammation, and coagulopathies (dysfunctions of the blood coagulation system) persist long after the initial infection. It bears similarities to other post-viral syndromes, and to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Many regulatory health bodies still do not recognize this syndrome as a separate disease entity, and refer to it under the broad terminology of 'COVID', although its demographics are quite different from those of acute COVID-19. A few years ago, we discovered that fibrinogen in blood can clot into an anomalous 'amyloid' form of fibrin that (like other β-rich amyloids and prions) is relatively resistant to proteolysis (fibrinolysis). The result, as is strongly manifested in platelet-poor plasma (PPP) of individuals with Long COVID, is extensive fibrin amyloid microclots that can persist, can entrap other proteins, and that may lead to the production of various autoantibodies. These microclots are more-or-less easily measured in PPP with the stain thioflavin T and a simple fluorescence microscope. Although the symptoms of Long COVID are multifarious, we here argue that the ability of these fibrin amyloid microclots (fibrinaloids) to block up capillaries, and thus to limit the passage of red blood cells and hence O2 exchange, can actually underpin the majority of these symptoms. Consistent with this, in a preliminary report, it has been shown that suitable and closely monitored 'triple' anticoagulant therapy that leads to the removal of the microclots also removes the other symptoms. Fibrin amyloid microclots represent a novel and potentially important target for both the understanding and treatment of Long COVID and related disorders.
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kemitorvet 200, 2800 Kgs Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, South Africa
| | | | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, South Africa
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17
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Stepanenko OV, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV, Sulatskaya AI. New findings on GFP-like protein application as fluorescent tags: Fibrillogenesis, oligomerization, and amorphous aggregation. Int J Biol Macromol 2021; 192:1304-1310. [PMID: 34687761 DOI: 10.1016/j.ijbiomac.2021.10.107] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/19/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
Green fluorescent proteins (GFP) are commonly used as fluorescent tags and biosensors in cell biology and medicine. However, the propensity of GFP-like proteins to aggregate and the consequence of intermolecular interaction for their application have not been thoroughly examined. In this work, alternative aggregation pathways of superfolder green fluorescent protein (sfGFP) were demonstrated using a spectroscopic and microscopic study of the samples prepared by equilibrium microdialysis. Besides oligomerization of native monomers, we showed for the first time the condition-specific formation by sfGFP of either amyloid fibrils (at increased temperature or acidity) or amorphous aggregates (at physiological conditions). Both types of sfGFP aggregates had lost green fluorescence and were toxic to cells. Thus, when using GFP-like proteins as fluorescent tags, one should take into account their high ability to form aggregates with lost unique visible fluorescence in the cellular environment, which affects cell viability. Moreover, the results of this work cast doubt on the correctness of the data on the fibrillogenesis of various amyloidogenic proteins obtained using their fusion with GFP-like proteins.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia.
| | - Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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18
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Zhytniakivska O, Kurutos A, Shchuka M, Vus K, Tarabara U, Trusova V, Gorbenko G. Fӧrster resonance energy transfer between Thioflavin T and unsymmetrical trimethine cyanine dyes on amyloid fibril scaffold. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Näsström T, Dahlberg T, Malyshev D, Ådén J, Andersson PO, Andersson M, Karlsson BCG. Synthetic NAC 71-82 Peptides Designed to Produce Fibrils with Different Protofilament Interface Contacts. Int J Mol Sci 2021; 22:ijms22179334. [PMID: 34502242 PMCID: PMC8431055 DOI: 10.3390/ijms22179334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Alpha-synucleinopathies are featured by fibrillar inclusions in brain cells. Although α-synuclein fibrils display structural diversity, the origin of this diversity is not fully understood. We used molecular dynamics simulations to design synthetic peptides, based on the NAC 71-82 amino acid fragment of α-synuclein, that govern protofilament contacts and generation of twisted fibrillar polymorphs. Four peptides with structures based on either single or double fragments and capped or non-capped ends were selected for further analysis. We determined the fibrillar yield and the structures from these peptides found in the solution after fibrillisation using protein concentration determination assay and circular dichroism spectroscopy. In addition, we characterised secondary structures formed by individual fibrillar complexes using laser-tweezers Raman spectroscopy. Results suggest less mature fibrils, based on the lower relative β-sheet content for double- than single-fragment peptide fibrils. We confirmed this structural difference by TEM analysis which revealed, in addition to short protofibrils, more elongated, twisted and rod-like fibril structures in non-capped and capped double-fragment peptide systems, respectively. Finally, time-correlated single-photon counting demonstrated a difference in the Thioflavin T fluorescence lifetime profiles upon fibril binding. It could be proposed that this difference originated from morphological differences in the fibril samples. Altogether, these results highlight the potential of using peptide models for the generation of fibrils that share morphological features relevant for disease, e.g., twisted and rod-like polymorphs.
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Affiliation(s)
- Thomas Näsström
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
| | - Tobias Dahlberg
- The Biophysics and Biophotonics Group, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden; (T.D.); (D.M.); (M.A.)
| | - Dmitry Malyshev
- The Biophysics and Biophotonics Group, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden; (T.D.); (D.M.); (M.A.)
| | - Jörgen Ådén
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden;
| | - Per Ola Andersson
- Department of Material Science and Engineering, Applied Materials Science, Uppsala University, SE-751 03 Uppsala, Sweden;
| | - Magnus Andersson
- The Biophysics and Biophotonics Group, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden; (T.D.); (D.M.); (M.A.)
| | - Björn C. G. Karlsson
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
- Correspondence:
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20
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Antonschmidt L, Dervişoğlu R, Sant V, Tekwani Movellan K, Mey I, Riedel D, Steinem C, Becker S, Andreas LB, Griesinger C. Insights into the molecular mechanism of amyloid filament formation: Segmental folding of α-synuclein on lipid membranes. SCIENCE ADVANCES 2021; 7:7/20/eabg2174. [PMID: 33990334 PMCID: PMC8121418 DOI: 10.1126/sciadv.abg2174] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/25/2021] [Indexed: 05/15/2023]
Abstract
Recent advances in the structural biology of disease-relevant α-synuclein fibrils have revealed a variety of structures, yet little is known about the process of fibril aggregate formation. Characterization of intermediate species that form during aggregation is crucial; however, this has proven very challenging because of their transient nature, heterogeneity, and low population. Here, we investigate the aggregation of α-synuclein bound to negatively charged phospholipid small unilamellar vesicles. Through a combination of kinetic and structural studies, we identify key time points in the aggregation process that enable targeted isolation of prefibrillar and early fibrillar intermediates. By using solid-state nuclear magnetic resonance, we show the gradual buildup of structural features in an α-synuclein fibril filament, revealing a segmental folding process. We identify distinct membrane-binding domains in α-synuclein aggregates, and the combined data are used to present a comprehensive mechanism of the folding of α-synuclein on lipid membranes.
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Affiliation(s)
- Leif Antonschmidt
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Rıza Dervişoğlu
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vrinda Sant
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, CA, USA
| | - Kumar Tekwani Movellan
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ingo Mey
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Göttingen, Germany
- Biomolecular Chemistry Group, Max-Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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21
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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22
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Stepanenko OV, Sulatsky MI, Mikhailova EV, Stepanenko OV, Povarova OI, Kuznetsova IM, Turoverov KK, Sulatskaya AI. Alpha-B-Crystallin Effect on Mature Amyloid Fibrils: Different Degradation Mechanisms and Changes in Cytotoxicity. Int J Mol Sci 2020; 21:ijms21207659. [PMID: 33081200 PMCID: PMC7589196 DOI: 10.3390/ijms21207659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022] Open
Abstract
Given the ability of molecular chaperones and chaperone-like proteins to inhibit the formation of pathological amyloid fibrils, the chaperone-based therapy of amyloidosis has recently been proposed. However, since these diseases are often diagnosed at the stages when a large amount of amyloids is already accumulated in the patient’s body, in this work we pay attention to the undeservedly poorly studied problem of chaperone and chaperone-like proteins’ effect on mature amyloid fibrils. We showed that a heat shock protein alpha-B-crystallin, which is capable of inhibiting fibrillogenesis and is found in large quantities as a part of amyloid plaques, can induce degradation of mature amyloids by two different mechanisms. Under physiological conditions, alpha-B-crystallin induces fluffing and unweaving of amyloid fibrils, which leads to a partial decrease in their structural ordering without lowering their stability and can increase their cytotoxicity. We found a higher correlation between the rate and effectiveness of amyloids degradation with the size of fibrils clusters rather than with amino acid sequence of amyloidogenic protein. Some external effects (such as an increase in medium acidity) can lead to a change in the mechanism of fibrils degradation induced by alpha-B-crystallin: amyloid fibers are fragmented without changing their secondary structure and properties. According to recent data, fibrils cutting can lead to the generation of seeds for new bona fide amyloid fibrils and accelerate the accumulation of amyloids, as well as enhance the ability of fibrils to disrupt membranes and to reduce cell viability. Our results emphasize the need to test the chaperone effect not only on fibrillogenesis, but also on the mature amyloid fibrils, including stress conditions, in order to avoid undesirable disease progression during chaperone-based therapy.
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Affiliation(s)
- Olga V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia; (O.V.S.); (E.V.M.); (O.V.S.); (O.I.P.); (I.M.K.); (A.I.S.)
| | - M. I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia;
| | - E. V. Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia; (O.V.S.); (E.V.M.); (O.V.S.); (O.I.P.); (I.M.K.); (A.I.S.)
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia; (O.V.S.); (E.V.M.); (O.V.S.); (O.I.P.); (I.M.K.); (A.I.S.)
| | - O. I. Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia; (O.V.S.); (E.V.M.); (O.V.S.); (O.I.P.); (I.M.K.); (A.I.S.)
| | - I. M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia; (O.V.S.); (E.V.M.); (O.V.S.); (O.I.P.); (I.M.K.); (A.I.S.)
| | - K. K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia; (O.V.S.); (E.V.M.); (O.V.S.); (O.I.P.); (I.M.K.); (A.I.S.)
- Peter the Great St.-Petersburg Polytechnic University, Polytechnicheskaya 29, 195251 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-812-297-19-57
| | - A. I. Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia; (O.V.S.); (E.V.M.); (O.V.S.); (O.I.P.); (I.M.K.); (A.I.S.)
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23
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Abdul Manap AS, Madhavan P, Vijayabalan S, Chia A, Fukui K. Explicating anti-amyloidogenic role of curcumin and piperine via amyloid beta (A β) explicit pathway: recovery and reversal paradigm effects. PeerJ 2020; 8:e10003. [PMID: 33062432 PMCID: PMC7532763 DOI: 10.7717/peerj.10003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 08/30/2020] [Indexed: 12/28/2022] Open
Abstract
Previously, we reported the synergistic effects of curcumin and piperine in cell cultures as potential anti-cholinesterase and anti-amyloidogenic agents. Due to limited findings on the enrolment of these compounds on epigenetic events in AD, we aimed at elucidating the expression profiles of Aβ42-induced SH-SY5Y cells using microarray profiling. In this study, an optimized concentration of 35 µM of curcumin and piperine in combination was used to treat Aβ42 fibril and high-throughput microarray profiling was performed on the extracted RNA. This was then compared to curcumin and piperine used singularly at 49.11 µM and 25 µM, respectively. Our results demonstrated that in the curcumin treated group, from the top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ -2), there were five upregulated and three downregulated genes involved in the amyloidogenic pathway. While from top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ - 2) in the piperine treated group, there were four upregulated and three downregulated genes involved in the same pathway, whereas there were five upregulated and two downregulated genes involved (p < 0.05; fold change ≥ 2 or ≤ - 2) in the curcumin-piperine combined group. Four genes namely GABARAPL1, CTSB, RAB5 and AK5 were expressed significantly in all groups. Other genes such as ITPR1, GSK3B, PPP3CC, ERN1, APH1A, CYCS and CALM2 were novel putative genes that are involved in the pathogenesis of AD. We revealed that curcumin and piperine have displayed their actions against Aβ via the modulation of various mechanistic pathways. Alterations in expression profiles of genes in the neuronal cell model may explain Aβ pathology post-treatment and provide new insights for remedial approaches of a combined treatment using curcumin and piperine.
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Affiliation(s)
- Aimi Syamima Abdul Manap
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Selangor, Malaysia
| | - Priya Madhavan
- School of Medicine, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Selangor, Malaysia
| | - Shantini Vijayabalan
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Selangor, Malaysia
| | - Adeline Chia
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Selangor, Malaysia
| | - Koji Fukui
- Department of Bioscience and Engineering, College of Systems Engineering and Science, Shibaura Institute of Technology, Saitama, Japan
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24
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Pravin N, Kumar R, Tripathi S, Kumar P, Mohite GM, Navalkar A, Panigrahi R, Singh N, Gadhe LG, Manchanda S, Shimozawa M, Nilsson P, Johansson J, Kumar A, Maji SK, Shanmugam M. Benzimidazole-based fluorophores for the detection of amyloid fibrils with higher sensitivity than Thioflavin-T. J Neurochem 2020; 156:1003-1019. [PMID: 32750740 DOI: 10.1111/jnc.15138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 07/14/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022]
Abstract
Protein aggregation into amyloid fibrils is a key feature of a multitude of neurodegenerative diseases such as Alzheimer's, Parkinson's, and Prion disease. To detect amyloid fibrils, fluorophores with high sensitivity and better efficiency coupled with the low toxicity are in high demand even to date. In this pursuit, we have unveiled two benzimidazole-based fluorescence sensors ([C15 H15 N3 ] (C1) and [C16 H16 N3 O2 ] (C2), which possess exceptional affinity toward different amyloid fibrils in its submicromolar concentration (8 × 10-9 M), whereas under a similar concentration, the gold standard Thioflavin-T (ThT) fails to bind with amyloid fibrils. These fluorescent markers bind to α-Syn amyloid fibrils as well as amyloid fibrils forming other proteins/peptides including Aβ42 amyloid fibrils. The 1 H-15 N heteronuclear quantum correlation spectroscopy nuclear magnetic resonance data collected on wild-type α-Syn monomer with and without the fluorophores (C1 and C2) reveal that there is weak or no interactions between C1 or C2 with residues in α-Syn monomer, which indirectly reflects the specific binding ability of C1 and C2 to the α-Syn amyloid fibrils. Detailed studies further suggest that C1 and C2 can detect/bind with the α-Syn amyloid fibril as low as 100 × 10-9 M. Extremely low or no cytotoxicity is observed for C1 and C2 and they do not interfere with α-Syn fibrillation kinetics, unlike ThT. Both C1/C2 not only shows selective binding with amyloid fibrils forming various proteins/peptides but also displays excellent affinity and selectivity toward α-Syn amyloid aggregates in SH-SY5Y cells and Aβ42 amyloid plaques in animal brain tissues. Overall, our data show that the developed dyes could be used for the detection of amyloid fibrils including α-Syn and Aβ42 amyloids with higher sensitivity as compared to currently used ThT.
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Affiliation(s)
- Narayanaperumal Pravin
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India.,Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Shalini Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Pardeep Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ganesh M Mohite
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Rajlaxmi Panigrahi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Namrata Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Laxmikant G Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Shaffi Manchanda
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Makoto Shimozawa
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Per Nilsson
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Jan Johansson
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Maheswaran Shanmugam
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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25
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Yu L, Zhang W, Luo W, Dupont RL, Xu Y, Wang Y, Tu B, Xu H, Wang X, Fang Q, Yang Y, Wang C, Wang C. Molecular recognition of human islet amyloid polypeptide assembly by selective oligomerization of thioflavin T. SCIENCE ADVANCES 2020; 6:eabc1449. [PMID: 32821844 PMCID: PMC7406363 DOI: 10.1126/sciadv.abc1449] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Selective oligomerization is a common phenomenon existing widely in the formation of intricate biological structures in nature. The precise design of drug molecules with an oligomerization state that specifically recognizes its receptor, however, remains substantially challenging. Here, we used scanning tunneling microscopy (STM) to identify the oligomerization states of an amyloid probe thioflavin T (ThT) on hIAPP8-37 assembly to be exclusively even numbers. We demonstrate that both adhesive interactions between ThT and the protein substrate and cohesive interactions among ThT molecules govern the oligomerization state of the bounded ThT. Specifically, the work of the cohesive interaction between two head/tail ThTs is determined to be 6.4 k B T, around 50% larger than that of the cohesive interaction between two side-by-side ThTs (4.2 k B T). Overall, our STM imaging and theoretical understanding at the single-molecule level provide valuable insights into the design of drug compounds using the selective oligomerization of molecular probes to recognize protein self-assembly.
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Affiliation(s)
- Lanlan Yu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Wenbo Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
| | - Wendi Luo
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Robert L. Dupont
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Yang Xu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Yibing Wang
- State Key Laboratory of Bioreactor Engineering, Biomedical Nanotechnology Center, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Bin Tu
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Haiyan Xu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, P. R. China
| | - Xiaoguang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Qiaojun Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Yanlian Yang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P. R. China
| | - Chenxuan Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P. R. China
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26
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Nachman E, Wentink AS, Madiona K, Bousset L, Katsinelos T, Allinson K, Kampinga H, McEwan WA, Jahn TR, Melki R, Mogk A, Bukau B, Nussbaum-Krammer C. Disassembly of Tau fibrils by the human Hsp70 disaggregation machinery generates small seeding-competent species. J Biol Chem 2020; 295:9676-9690. [PMID: 32467226 PMCID: PMC7363153 DOI: 10.1074/jbc.ra120.013478] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/17/2020] [Indexed: 12/14/2022] Open
Abstract
The accumulation of amyloid Tau aggregates is implicated in Alzheimer's disease (AD) and other tauopathies. Molecular chaperones are known to maintain protein homeostasis. Here, we show that an ATP-dependent human chaperone system disassembles Tau fibrils in vitro We found that this function is mediated by the core chaperone HSC70, assisted by specific cochaperones, in particular class B J-domain proteins and a heat shock protein 110 (Hsp110)-type nucleotide exchange factor (NEF). The Hsp70 disaggregation machinery processed recombinant fibrils assembled from all six Tau isoforms as well as Sarkosyl-resistant Tau aggregates extracted from cell cultures and human AD brain tissues, demonstrating the ability of the Hsp70 machinery to recognize a broad range of Tau aggregates. However, the chaperone activity released monomeric and small oligomeric Tau species, which induced the aggregation of self-propagating Tau conformers in a Tau cell culture model. We conclude that the activity of the Hsp70 disaggregation machinery is a double-edged sword, as it eliminates Tau amyloids at the cost of generating new seeds.
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Affiliation(s)
- Eliana Nachman
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.,Schaller Research Group Proteostasis in Neurodegenerative Disease of Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anne S Wentink
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Karine Madiona
- Institute Francois Jacob (MIRCen), CEA, and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-Aux-Roses, France
| | - Luc Bousset
- Institute Francois Jacob (MIRCen), CEA, and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-Aux-Roses, France
| | - Taxiarchis Katsinelos
- Department of Clinical Neurosciences, UK Dementia Research Institute at the University of Cambridge, Cambridge, United Kingdom
| | - Kieren Allinson
- Department of Neuropathology, Cambridge Universities Hospital Trust, Cambridge, United Kingdom
| | - Harm Kampinga
- Department of Biomedical Science of Cell and System, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - William A McEwan
- Department of Clinical Neurosciences, UK Dementia Research Institute at the University of Cambridge, Cambridge, United Kingdom
| | - Thomas R Jahn
- Schaller Research Group Proteostasis in Neurodegenerative Disease of Heidelberg University and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ronald Melki
- Institute Francois Jacob (MIRCen), CEA, and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-Aux-Roses, France
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Carmen Nussbaum-Krammer
- Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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27
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Chen Y, Peng F, Su T, Yang H, Qiu F. Direct Identification of Amyloid Peptide Fragments in Human α-Synuclein Based on Consecutive Hydrophobic Amino Acids. ACS OMEGA 2020; 5:11677-11686. [PMID: 32478258 PMCID: PMC7254785 DOI: 10.1021/acsomega.0c00979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/04/2020] [Indexed: 02/08/2023]
Abstract
![]()
Formation of amyloid fibrils by misfolding
α-synuclein is
a characteristic feature of Parkinson’s disease, but the exact
molecular mechanism of this process has long been an unresolved mystery.
Identification of critical amyloid peptide fragments from α-synuclein
may hold the key to decipher this mystery. Focusing on consecutive
hydrophobic amino acids (CHAA) in the protein sequence, in this study
we proposed a sequence-based strategy for direct identification of
amyloid peptide fragments in α-synuclein. We picked out three
CHAA fragments (two hexapeptides and one tetrapeptide) from α-synuclein
and studied their amyloidogenic property. The thioflavin-T binding
test, transmission electron microscopy, Congo red staining, and Fourier
transform infrared spectroscopy revealed that although only hexapeptides
could undergo amyloid aggregation on their own, extended peptide fragments
based on any of the three peptides could form typical amyloid fibrils.
Primary amyloidogenic fragments based on the three peptides showed
synergetic aggregation behavior and could accelerate the aggregation
of full-length α-synuclein. It was proved that hydrophobic interaction
played a predominant role for the aggregation of these peptides and
full-length α-synuclein. A central alanine-to-lysine substitution
in each hydrophobic fragment completely eliminated the peptides’
amyloidogenic property, and alanine-to-lysine substitutions at corresponding
sites in full-length α-synuclein also decreased the protein’s
amyloidogenic potency. These findings suggested that CHAA fragments
were potentially amyloidogenic and played an important role for the
aggregation of α-synuclein. The identification of these fragments
might provide helpful information for eventually clarifying the molecular
mechanism of α-synuclein aggregation. On the other hand, our
study suggested that the CHAA fragment might be a simple motif for
direct sequence-based identification of amyloid peptides.
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Affiliation(s)
- Yongzhu Chen
- Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
- Periodical Press of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fei Peng
- Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Su
- West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Yang
- Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Feng Qiu
- Laboratory of Anesthesia and Critical Care Medicine, Translational Neuroscience Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu 610041, China
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28
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Lengyel-Zhand Z, Ferrie JJ, Janssen B, Hsieh CJ, Graham T, Xu KY, Haney CM, Lee VMY, Trojanowski JQ, Petersson EJ, Mach RH. Synthesis and characterization of high affinity fluorogenic α-synuclein probes. Chem Commun (Camb) 2020; 56:3567-3570. [PMID: 32104795 PMCID: PMC7717557 DOI: 10.1039/c9cc09849f] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescent small molecules are powerful tools for imaging α-synuclein pathology in vitro and in vivo. In this work, we explore benzofuranone as a potential scaffold for the design of fluorescent α-synuclein probes. These compounds have high affinity for α-synuclein, show fluorescent turn-on upon binding to fibrils, and display different binding to Lewy bodies, Lewy neurites and glial cytoplasmic inclusion pathologies in post-mortem brain tissue. These studies not only reveal the potential of benzofuranone compounds as α-synuclein specific fluorescent probes, but also have implications for the ways in which α-synucleinopathies are conformationally different and display distinct small molecule binding sites.
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Affiliation(s)
- Zsofia Lengyel-Zhand
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - John J Ferrie
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Bieneke Janssen
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Chia-Ju Hsieh
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Thomas Graham
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kui-Ying Xu
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Conor M Haney
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Virginia M-Y Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Robert H Mach
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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29
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Sancataldo G, Anselmo S, Vetri V. Phasor-FLIM analysis of Thioflavin T self-quenching in Concanavalin amyloid fibrils. Microsc Res Tech 2020; 83:811-816. [PMID: 32180304 DOI: 10.1002/jemt.23472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 02/28/2020] [Indexed: 12/20/2022]
Abstract
The formation of amyloid structures has traditionally been related to human neurodegenerative pathologies and, in recent years, the interest in these highly stable nanostructures was extended to biomaterial sciences. A common method to monitor amyloid growth is the analysis of Thioflavin T fluorescence. The use of this highly selective dye, diffused worldwide, allows mechanistic studies of supramolecular assemblies also giving back important insight on the structure of these aggregates. Here we present experimental evidence of self-quenching effect of Thioflavin T in presence of amyloid fibrils. A significant reduction of fluorescence lifetime of this dye which is not related to the properties of analyzed amyloid structures is found. This result is achieved by coupling Fluorescence Lifetime Imaging Microscopy with phasor approach as suitable model-free methods and constitute a serious warning that have to be taken in account if is dye is used for quantitative studies.
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Affiliation(s)
- Giuseppe Sancataldo
- Dipartimento di Fisica e Chimica - E. Segrè, Università di Palermo, Palermo, Italy
| | - Sara Anselmo
- Dipartimento di Fisica e Chimica - E. Segrè, Università di Palermo, Palermo, Italy
| | - Valeria Vetri
- Dipartimento di Fisica e Chimica - E. Segrè, Università di Palermo, Palermo, Italy
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30
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Scutellarin inhibits the uninduced and metal-induced aggregation of α-Synuclein and disaggregates preformed fibrils: implications for Parkinson's disease. Biochem J 2020; 477:645-670. [DOI: 10.1042/bcj20190705] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 01/07/2023]
Abstract
The aggregation of the protein alpha synuclein (α-Syn), a known contributor in Parkinson's disease (PD) pathogenesis is triggered by transition metal ions through occupational exposure and disrupted metal ion homeostasis. Naturally occurring small molecules such as polyphenols have emerged as promising inhibitors of α-Syn fibrillation and toxicity and could be potential therapeutic agents against PD. Here, using an array of biophysical tools combined with cellular assays, we demonstrate that the novel polyphenolic compound scutellarin efficiently inhibits the uninduced and metal-induced fibrillation of α-Syn by acting at the nucleation stage and stabilizes a partially folded intermediate of α-Syn to form SDS-resistant, higher-order oligomers (∼680 kDa) and also disaggregates preformed fibrils of α-Syn into similar type of higher-order oligomers. ANS binding assay, fluorescence lifetime measurements and cell-toxicity experiments reveal scutellarin-generated oligomers as compact, low hydrophobicity structures with modulated surface properties and significantly reduced cytotoxicity than the fibrillation intermediates of α-Syn control. Fluorescence spectroscopy and isothermal titration calorimetry establish the binding between scutellarin and α-Syn to be non-covalent in nature and of moderate affinity (Ka ∼ 105 M−1). Molecular docking approaches suggest binding of scutellarin to the residues present in the NAC region and C-terminus of monomeric α-Syn and the C-terminal residues of fibrillar α-Syn, demonstrating inhibition of fibrillation upon binding to these residues and possible stabilization of the autoinhibitory conformation of α-Syn. These findings reveal interesting insights into the mechanism of scutellarin action and establish it as an efficient modulator of uninduced as well as metal-induced α-Syn fibrillation and toxicity.
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Bondia P, Torra J, Tone CM, Sawazaki T, del Valle A, Sot B, Nonell S, Kanai M, Sohma Y, Flors C. Nanoscale View of Amyloid Photodynamic Damage. J Am Chem Soc 2019; 142:922-930. [DOI: 10.1021/jacs.9b10632] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Patricia Bondia
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia), C/Faraday 9, Madrid 28049, Spain
| | - Joaquim Torra
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia), C/Faraday 9, Madrid 28049, Spain
| | - Caterina M. Tone
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia), C/Faraday 9, Madrid 28049, Spain
| | - Taka Sawazaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adrián del Valle
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia), C/Faraday 9, Madrid 28049, Spain
| | - Begoña Sot
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia), C/Faraday 9, Madrid 28049, Spain
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona 08017, Spain
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Youhei Sohma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Cristina Flors
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanociencia), C/Faraday 9, Madrid 28049, Spain
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Näsström T, Andersson PO, Lejon C, Karlsson BCG. Amyloid fibrils prepared using an acetylated and methyl amidated peptide model of the α-Synuclein NAC 71-82 amino acid stretch contain an additional cross-β structure also found in prion proteins. Sci Rep 2019; 9:15949. [PMID: 31685848 PMCID: PMC6828723 DOI: 10.1038/s41598-019-52206-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/15/2019] [Indexed: 11/09/2022] Open
Abstract
The 71-82 fragment of the non-amyloid-β component (NAC) region of the Parkinson's disease (PD) and dementia with Lewy bodies (DLB) related protein α-Synuclein, has been reported to be important during protein misfolding. Although reports have demonstrated the importance of this fragment for the aggregation properties of the full-length protein, its exact role in pre-fibrillar oligomerisation, fibrillar growth and morphology has not yet been fully elucidated. Here, we provide evidence that fibrils prepared from an acetylated and methyl amidated peptide of the NAC 71-82 amino acid stretch of α-Synuclein are amyloid and contain, in addition to the cross-β structure detected in the full-length protein fibrils, a cross-β structure previously observed in prion proteins. These results shed light on the aggregation propensity of the NAC 71-82 amino acid stretch of the full-length protein but also the roles of the N- and C-terminal domains of α-Synuclein in balancing this aggregation propensity. The results also suggest that early aggregated forms of the capped NAC 71-82 peptide generated structures were stabilised by an anti-parallel and twisted β-sheet motif. Due to its expected toxicity, this β-sheet motif may be a promising molecular target for the development of therapeutic strategies for PD and DLB.
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Affiliation(s)
- Thomas Näsström
- Neurodegenerative Disorders Unit, Linnæus University, SE-392 31, Kalmar, Sweden.
| | - Per Ola Andersson
- FOI Swedish Defence Research Agency, CBRN Defence & Security, SE-901 82, Umeå, Sweden.,Department of Engineering Sciences: Applied Material Science, Uppsala University, SE-751 21, Uppsala, Sweden
| | - Christian Lejon
- FOI Swedish Defence Research Agency, CBRN Defence & Security, SE-901 82, Umeå, Sweden
| | - Björn C G Karlsson
- Physical Pharmacy Laboratory, Linnæus University Centre for Biomaterials Chemistry, Linnæus University, SE-392 31, Kalmar, Sweden.
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Ziaunys M, Smirnovas V. Additional Thioflavin-T Binding Mode in Insulin Fibril Inner Core Region. J Phys Chem B 2019; 123:8727-8732. [PMID: 31580671 DOI: 10.1021/acs.jpcb.9b08652] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloidogenic protein aggregation into fibrils is linked to several neurodegenerative disorders, such as Alzheimer's or Parkinson's disease. An amyloid specific fluorescent dye thioflavin-T (ThT) is often used to track the formation of these fibrils in vitro. Despite its wide application, it is still unknown how many types of ThT binding modes to amyloids exist, with multiple studies indicating varying numbers. In this work, we examine the binding of ThT to insulin fibrils generated at pH 2.4 and reveal a possible inner core binding mode which is not accessible to the dye molecule after aggregation occurs.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center , Vilnius University , Vilnius LT-10257 , Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center , Vilnius University , Vilnius LT-10257 , Lithuania
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Roy D, Bhattacharyya D, Bhunia A. Do Catechins (ECG and EGCG) Bind to the Same Site as Thioflavin T (ThT) in Amyloid Fibril? Answer From Saturation Transfer Difference NMR. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Dipanwita Roy
- Department of Biophysics, Bose Institute, Kolkata, WB, India
| | | | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, WB, India
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Aranda-Souza MÂ, Lorena VMBD, Correia MTDS, Pereira-Neves A, Figueiredo RCBQD. A C-type lectin from Bothrops leucurus snake venom forms amyloid-like aggregates in RPMI medium and are efficiently phagocytosed by peritoneal macrophages. Toxicon 2019; 157:93-100. [DOI: 10.1016/j.toxicon.2018.11.309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 12/16/2022]
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Sulatskaya AI, Rodina NP, Polyakov DS, Sulatsky MI, Artamonova TO, Khodorkovskii MA, Shavlovsky MM, Kuznetsova IM, Turoverov KK. Structural Features of Amyloid Fibrils Formed from the Full-Length and Truncated Forms of Beta-2-Microglobulin Probed by Fluorescent Dye Thioflavin T. Int J Mol Sci 2018; 19:E2762. [PMID: 30223436 PMCID: PMC6164334 DOI: 10.3390/ijms19092762] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/04/2018] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
The persistence of high concentrations of beta-2-microglobulin (β2M) in the blood of patients with acute renal failure leads to the development of the dialysis-related amyloidosis. This disease manifests in the deposition of amyloid fibrils formed from the various forms of β2M in the tissues and biological fluids of patients. In this paper, the amyloid fibrils formed from the full-length β2M (β2m) and its variants that lack the 6 and 10 N-terminal amino acids of the protein polypeptide chain (ΔN6β2m and ΔN10β2m, respectively) were probed by using the fluorescent dye thioflavin T (ThT). For this aim, the tested solutions were prepared via the equilibrium microdialysis approach. Spectroscopic analysis of the obtained samples allowed us to detect one binding mode (type) of ThT interaction with all the studied variants of β2M amyloid fibrils with affinity ~10⁴ M-1. This interaction can be explained by the dye molecules incorporation into the grooves that were formed by the amino acids side chains of amyloid protofibrils along the long axis of the fibrils. The decrease in the affinity and stoichiometry of the dye interaction with β2M fibrils, as well as in the fluorescence quantum yield and lifetime of the bound dye upon the shortening of the protein amino acid sequence were shown. The observed differences in the ThT-β2M fibrils binding parameters and characteristics of the bound dye allowed to prove not only the difference of the ΔN10β2m fibrils from other β2M fibrils (that can be detected visually, for example, by transmission electron microscopy (TEM), but also the differences between β2m and ΔN6β2m fibrils (that can not be unequivocally confirmed by other approaches). These results prove an essential role of N-terminal amino acids of the protein in the formation of the β2M amyloid fibrils. Information about amyloidogenic protein sequences can be claimed in the development of ways to inhibit β2M fibrillogenesis for the treatment of dialysis-related amyloidosis.
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Affiliation(s)
- Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Science, Tikhoretsky ave. 4, St. Petersburg 194064, Russia.
| | - Natalia P Rodina
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Science, Tikhoretsky ave. 4, St. Petersburg 194064, Russia.
| | - Dmitry S Polyakov
- Department of Molecular Genetics, Institute of Experimental Medicine, Pavlov str. 12, St. Petersburg 197376, Russia.
- Chair of Medical Genetics, North-Western State Medical University named after I.I. Mechnikov, Piskarevskij prospect 47, St. Petersburg 195067, Russia.
| | - Maksim I Sulatsky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Science, Tikhoretsky ave. 4, St. Petersburg 194064, Russia.
| | - Tatyana O Artamonova
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russia.
| | - Mikhail A Khodorkovskii
- Research Center of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russia.
| | - Mikhail M Shavlovsky
- Department of Molecular Genetics, Institute of Experimental Medicine, Pavlov str. 12, St. Petersburg 197376, Russia.
- Chair of Medical Genetics, North-Western State Medical University named after I.I. Mechnikov, Piskarevskij prospect 47, St. Petersburg 195067, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Science, Tikhoretsky ave. 4, St. Petersburg 194064, Russia.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Science, Tikhoretsky ave. 4, St. Petersburg 194064, Russia.
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russia.
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