1
|
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 DOI: 10.1021/acs.jpclett.4c00699] [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: 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.
Collapse
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
| |
Collapse
|
2
|
Sulatskaya AI, Rodina NP, Polyakov DS, Sulatsky MI, Artamonova TO, Khodorkovskii MA, Shavlovsky MM, Kuznetsova IM, Turoverov KK. Correction: Sulatskaya et al. 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, 2762. Int J Mol Sci 2024; 25:6411. [PMID: 38928519 PMCID: PMC11203428 DOI: 10.3390/ijms25126411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024] Open
Abstract
In the original publication [...].
Collapse
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; (A.I.S.)
| | - 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; (A.I.S.)
| | - 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; (A.I.S.)
| | - 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; (A.I.S.)
| | - 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; (A.I.S.)
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russia
| |
Collapse
|
3
|
Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Structure and Polymorphism of Amyloid and Amyloid-Like Aggregates. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:450-463. [PMID: 35790379 DOI: 10.1134/s0006297922050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Amyloids are protein aggregates with the cross-β structure. The interest in amyloids is explained, on the one hand, by their role in the development of socially significant human neurodegenerative diseases, and on the other hand, by the discovery of functional amyloids, whose formation is an integral part of cellular processes. To date, more than a hundred proteins with the amyloid or amyloid-like properties have been identified. Studying the structure of amyloid aggregates has revealed a wide variety of protein conformations. In the review, we discuss the diversity of protein folds in the amyloid-like aggregates and the characteristic features of amyloid aggregates that determine their unusual properties, including stability and interaction with amyloid-specific dyes. The review also describes the diversity of amyloid aggregates and its significance for living organisms.
Collapse
Affiliation(s)
- Anton B Matiiv
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Nina P Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Bioinformatics Institute, Saint Petersburg, 197342, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
- Laboratory of Amyloid Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia
| |
Collapse
|
4
|
Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021; 60:15445-15451. [PMID: 33891789 DOI: 10.1002/anie.202102408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/19/2021] [Indexed: 11/08/2022]
Abstract
Pulsed-field gradient (PFG) NMR is an important tool for characterization of biomolecules and supramolecular assemblies. However, for micrometer-sized objects, such as amyloid fibrils, these experiments become difficult to interpret because in addition to translational diffusion they are also sensitive to rotational diffusion. We have constructed a mathematical theory describing the outcome of PFG NMR experiments on rod-like fibrils. To test its validity, we have studied the fibrils formed by Sup35NM segment of the prion protein Sup35. The interpretation of the PFG NMR data in this system is fully consistent with the evidence from electron microscopy. Contrary to some previously expressed views, the signals originating from disordered regions in the fibrils can be readily differentiated from the similar signals representing small soluble species (e.g. proteolytic fragments). This paves the way for diffusion-sorted NMR experiments on complex amyloidogenic samples.
Collapse
Affiliation(s)
- Boris B Kharkov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia.,Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608, St. Petersburg, Russia
| | - Vladislav A Salikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, 199034, St. Petersburg, Russia.,Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
5
|
Kharkov BB, Podkorytov IS, Bondarev SA, Belousov MV, Salikov VA, Zhouravleva GA, Skrynnikov NR. The Role of Rotational Motion in Diffusion NMR Experiments on Supramolecular Assemblies: Application to Sup35NM Fibrils. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Boris B. Kharkov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Ivan S. Podkorytov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
- Laboratory for Proteomics of Supra-Organismal Systems All-Russia Research Institute for Agricultural Microbiology (ARRIAM) 196608 St. Petersburg Russia
| | - Vladislav A. Salikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology St. Petersburg State University 199034 St. Petersburg Russia
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR St. Petersburg State University 199034 St. Petersburg Russia
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| |
Collapse
|
6
|
Effect of Ionic Strength on Thioflavin-T Affinity to Amyloid Fibrils and Its Fluorescence Intensity. Int J Mol Sci 2020; 21:ijms21238916. [PMID: 33255444 PMCID: PMC7727833 DOI: 10.3390/ijms21238916] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
The formation of amyloid fibrils is linked to multiple neurodegenerative disorders, including Alzheimer’s and Parkinson’s disease. Despite years of research and countless studies on the topic of such aggregate formation, as well as their resulting structure, the current knowledge is still fairly limited. One of the main aspects prohibiting effective aggregation tracking is the environment’s effect on amyloid-specific dyes, namely thioflavin-T (ThT). Currently, there are only a few studies hinting at ionic strength being one of the factors that modulate the dye’s binding affinity and fluorescence intensity. In this work we explore this effect under a range of ionic strength conditions, using insulin, lysozyme, mouse prion protein, and α-synuclein fibrils. We show that ionic strength is an extremely important factor affecting both the binding affinity, as well as the fluorescence intensity of ThT.
Collapse
|
7
|
Ziaunys M, Sakalauskas A, Smirnovas V. Identifying Insulin Fibril Conformational Differences by Thioflavin-T Binding Characteristics. Biomacromolecules 2020; 21:4989-4997. [PMID: 33201685 PMCID: PMC7739267 DOI: 10.1021/acs.biomac.0c01178] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Amyloidogenic
protein aggregation into highly structured fibrils
is linked to more than 30 amyloidoses, including several neurodegenerative
disorders. Despite significant progress in trying to understand the
process of amyloid formation, there is still no cure or effective
treatment available. A number of studies involving potential anti-amyloid
compounds rely on the use of a fluorescent probe—thioflavin-T—to
track the appearance, growth, or disassembly of these cytotoxic aggregates.
Despite the wide application of this dye molecule, its interaction
with amyloid fibrils is still poorly understood. Recent reports have
shown it may possess distinct binding modes and fluorescence intensities
based on the conformation of the examined fibrils. In this work, we
generate insulin fibrils under four different conditions and attempt
to identify distinct conformations using both classic methods, such
as atomic force microscopy and Fourier-transform infrared spectroscopy,
as well as their ThT binding ability and fluorescence quantum yield.
We show that there is a significant variance of ThT fluorescence quantum
yields, excitation/emission maxima positions, and binding modes between
distinct insulin fibril conformations.
Collapse
Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio al. 7, Vilnius LT-10257, Lithuania
| |
Collapse
|
8
|
Sulatskaya AI, Bondarev SA, Sulatsky MI, Trubitsina NP, Belousov MV, Zhouravleva GA, Llanos MA, Kajava AV, Kuznetsova IM, Turoverov KK. Point mutations affecting yeast prion propagation change the structure of its amyloid fibrils. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Barbitoff YA, Matveenko AG, Bondarev SA, Maksiutenko EM, Kulikova AV, Zhouravleva GA. Quantitative assessment of chaperone binding to amyloid aggregates identifies specificity of Hsp40 interaction with yeast prion fibrils. FEMS Yeast Res 2020; 20:5831717. [PMID: 32379306 DOI: 10.1093/femsyr/foaa025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/05/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast self-perpetuating protein aggregates (yeast prions) provide a framework to investigate the interaction of misfolded proteins with the protein quality control machinery. The major component of this system that facilitates propagation of all known yeast amyloid prions is the Hsp104 chaperone that catalyzes fibril fragmentation. Overproduction of Hsp104 cures some yeast prions via a fragmentation-independent mechanism. Importantly, major cytosolic chaperones of the Hsp40 group, Sis1 and Ydj1, oppositely affect yeast prion propagation, and are capable of stimulating different activities of Hsp104. In this work, we developed a quantitative method to investigate the Hsp40 binding to amyloid aggregates. We demonstrate that Sis1 binds fibrils formed by the Sup35NM protein with higher affinity compared to Ydj1. Moreover, the interaction of Sis1 with the fibrils formed by the other yeast prion protein, Rnq1, is orders of magnitude weaker. We show that the deletion of the dimerization domain of Sis1 (crucial for the curing of [PSI+] by excess Hsp104) decreases its affinity to both Sup35NM and Rnq1 fibrils. Taken together, these results suggest that tight binding of Hsp40 to the amyloid fibrils is likely to enhance aggregate malpartition instead of fibril fragmentation.
Collapse
Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Evgeniia M Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| | - Alexandra V Kulikova
- Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya ul. 29, St. Petersburg, 195251 Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, 199034 Russia
| |
Collapse
|
10
|
Sulatsky MI, Sulatskaya AI, Stepanenko OV, Povarova OI, Kuznetsova IM, Turoverov KK. Denaturant effect on amyloid fibrils: Declasterization, depolymerization, denaturation and reassembly. Int J Biol Macromol 2020; 150:681-694. [PMID: 32057863 DOI: 10.1016/j.ijbiomac.2020.01.290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/07/2023]
Abstract
Accumulation of amyloid fibrils in organism accompanies many serious diseases, such as Alzheimer's and Parkinson's diseases, diabetes, prion diseases, etc. It is generally accepted that amyloids are highly resistant to degradation, which complicates their elimination in vivo and is one of the reasons for their pathogenicity. However, using a wide range of physicochemical approaches and specially elaborated method for the tested samples preparation by equilibrium microdialysis technique, it is proved that the stability of amyloids is greatly exaggerated. It turned out that amyloid fibrils formed from at least two amyloidogenic proteins, one of which is a model object for fibrils studying and the second is the cause of hemodialysis amyloidosis in an acute renal failure, are less stable than monomeric proteins. A mechanism of the degradation/reassembly of amyloid fibrils was proposed. It was shown that amyloid «seed» is a factor affecting not only the rate of the fibrils formation, but also their structure. Obtained results are a step towards identifying effects that can lead to degradation of amyloids and their clearance without adverse influence on the functionally active state of the protein or to change the structure and, as a result, the pathogenicity of these protein aggregates.
Collapse
Affiliation(s)
- M I Sulatsky
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - A I Sulatskaya
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - Olga V Stepanenko
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - O I Povarova
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - I M Kuznetsova
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - K K Turoverov
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia; Peter the Great St.-Petersburg Polytechnic University, St. Petersburg, Polytechnicheskaya 29, 195251, Russia.
| |
Collapse
|
11
|
Sulatsky MI, Sulatskaya AI, Povarova OI, Antifeeva IA, Kuznetsova IM, Turoverov KK. Effect of the fluorescent probes ThT and ANS on the mature amyloid fibrils. Prion 2020; 14:67-75. [PMID: 32008441 PMCID: PMC7009331 DOI: 10.1080/19336896.2020.1720487] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Fluorescent probes thioflavin T (ThT) and 1-anilino-8-naphthalene sulfonate (ANS) are widely used to study amyloid fibrils that accumulate in the body of patients with serious diseases, such as Alzheimer’s, Parkinson’s, prion diseases, etc. However, the possible effect of these probes on amyloid fibrils is not well understood. In this work, we investigated the photophysical characteristics, structure, and morphology of mature amyloid fibrils formed from two model proteins, insulin and lysozyme, in the presence of ThT and ANS. It turned out that ANS affects the secondary structure of amyloids (shown for fibrils formed from insulin and lysozyme) and their fibers clusterization (valid for lysozyme fibrils), while ThT has no such effects. These results confirm the differences in the mechanisms of these dyes interaction with amyloid fibrils. Observed effect of ANS was explained by the electrostatic interactions between the dye molecule and cationic groups of amyloid-forming proteins (unlike hydrophobic binding of ThT) that induce amyloids conformational changes. This interaction leads to weakening repulsion between positive charges of amyloid fibrils and can promote their clusterization. It was shown that when fibrillogenesis conditions and, consequently, fibrils structure is changing, as well as during defragmentation of amyloids by ultrasonication, the influence of ANS to amyloids does not change, which indicates the universality of the detected effects. Based on the obtained results, it was concluded that ANS should be used cautiously for the study of amyloid fibrils, since this fluorescence probe have a direct effect on the object of study.
Collapse
Affiliation(s)
- M I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - A I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - O I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - Iu A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - I M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia
| | - K K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology Russian Academy of Science, St. Petersburg, Russia.,Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| |
Collapse
|
12
|
Brown JWP, Bauer A, Polinkovsky ME, Bhumkar A, Hunter DJB, Gaus K, Sierecki E, Gambin Y. Single-molecule detection on a portable 3D-printed microscope. Nat Commun 2019; 10:5662. [PMID: 31827096 PMCID: PMC6906517 DOI: 10.1038/s41467-019-13617-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 11/08/2019] [Indexed: 11/22/2022] Open
Abstract
Single-molecule assays have, by definition, the ultimate sensitivity and represent the next frontier in biological analysis and diagnostics. However, many of these powerful technologies require dedicated laboratories and trained personnel and have therefore remained research tools for specialists. Here, we present a single-molecule confocal system built from a 3D-printed scaffold, resulting in a compact, plug and play device called the AttoBright. This device performs single photon counting and fluorescence correlation spectroscopy (FCS) in a simple format and is widely applicable to the detection of single fluorophores, proteins, liposomes or bacteria. The power of single-molecule detection is demonstrated by detecting single α-synuclein amyloid fibrils, that are currently evaluated as biomarkers for Parkinson’s disease, with an improved sensitivity of >100,000-fold over bulk measurements. Single-molecule in vitro assays require dedicated confocal microscopes equipped with fluorescence correlation spectroscopy (FCS) modules. Here the authors present a compact, cheap and open-source 3D-printed confocal microscope for single photon counting and FCS measurements, and use it to detect α-synuclein aggregation.
Collapse
Affiliation(s)
- James W P Brown
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Arnaud Bauer
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Mark E Polinkovsky
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Akshay Bhumkar
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Dominic J B Hunter
- The Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, University of New South Wales, Sydney, 2052, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, 2052, NSW, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, University of New South Wales, Sydney, 2052, NSW, Australia.
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, University of New South Wales, Sydney, 2052, NSW, Australia.
| |
Collapse
|
13
|
The Environment Is a Key Factor in Determining the Anti-Amyloid Efficacy of EGCG. Biomolecules 2019; 9:biom9120855. [PMID: 31835741 PMCID: PMC6995563 DOI: 10.3390/biom9120855] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/06/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
Millions of people around the world suffer from amyloid-related disorders, including Alzheimer's and Parkinson's diseases. Despite significant and sustained efforts, there are still no disease-modifying drugs available for the majority of amyloid-related disorders, and the overall failure rate in clinical trials is very high, even for compounds that show promising anti-amyloid activity in vitro. In this study, we demonstrate that even small changes in the chemical environment can strongly modulate the inhibitory effects of anti-amyloid compounds. Using one of the best-established amyloid inhibitory compounds, epigallocatechin-3-gallate (EGCG), as an example, and two amyloid-forming proteins, insulin and Parkinson's disease-related α -synuclein, we shed light on the previously unexplored sensitivity to solution conditions of the action of this compound on amyloid fibril formation. In the case of insulin, we show that the classification of EGCG as an amyloid inhibitor depends on the experimental conditions select, on the method used for the evaluation of the efficacy, and on whether or not EGCG is allowed to oxidise before the experiment. For α -synuclein, we show that a small change in pH value, from 7 to 6, transforms EGCG from an efficient inhibitor to completely ineffective, and we were able to explain this behaviour by the increased stability of EGCG against oxidation at pH 6.
Collapse
|
14
|
Sidhu A, Vaneyck J, Blum C, Segers-Nolten I, Subramaniam V. Polymorph-specific distribution of binding sites determines thioflavin-T fluorescence intensity in α-synuclein fibrils. Amyloid 2018; 25:189-196. [PMID: 30486688 DOI: 10.1080/13506129.2018.1517736] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Thioflavin-T (ThT) is the most commonly used fluorescent dye for following amyloid formation semi-quantitatively in vitro, specifically probing the fibrillar cross-β-sheet content. In recent years, structural polymorphism of amyloid fibrils has been shown to be an important aspect of amyloid formation, both in vitro and in neurodegenerative diseases. Therefore, understanding ThT-amyloid interactions in the context of structural polymorphism of amyloids is necessary for correct interpretation of ThT fluorescence data. Here we study the influence of fibril morphology on ThT fluorescence and ThT binding sites, with two morphologically distinct but chemically identical α-synuclein polymorphs. In ThT fluorescence assays the two polymorphs show type-specific fluorescence intensity behaviour although their β-sheet content has been shown to be similar. Further, fluorescence lifetime measurements of fibril-bound ThT reveal the presence of at least two qualitatively different ThT binding sites on the polymorphs. The relative distributions of the binding sites on the fibril surfaces appear to be morphology dependent, thus determining the observed polymorph-specific ThT fluorescence intensities. These results, highlighting the role of fibril morphology in ThT-based amyloid studies, underline the relevance of polymorphs in ThT-amyloid interaction and can explain the variability often observed in ThT amyloid binding assays.
Collapse
Affiliation(s)
- Arshdeep Sidhu
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Jonathan Vaneyck
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Christian Blum
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Ine Segers-Nolten
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Vinod Subramaniam
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands.,b Executive Board, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
| |
Collapse
|
15
|
Investigation of α-Synuclein Amyloid Fibrils Using the Fluorescent Probe Thioflavin T. Int J Mol Sci 2018; 19:ijms19092486. [PMID: 30142878 PMCID: PMC6163839 DOI: 10.3390/ijms19092486] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/08/2018] [Accepted: 08/20/2018] [Indexed: 11/29/2022] Open
Abstract
In this work, α-synuclein amyloid fibrils—the formation of which is a biomarker of Parkinson’s disease—were investigated using the fluorescent probe thioflavin T (ThT). The experimental conditions of protein fibrillogenesis were chosen so that a sufficient number of continuous measurements could be performed to characterize and analyze all stages of this process. The reproducibility of fibrillogenesis and the structure of the obtained aggregates (which is a critical point for further investigation) were proven using a wide range of physical-chemical methods. For the determination of ThT-α-synuclein amyloid fibril binding parameters, the sample and reference solutions were prepared using equilibrium microdialysis. By utilizing absorption spectroscopy of these solutions, the ThT-fibrils binding mode with a binding constant of about 104 M−1 and stoichiometry of ThT per protein molecule of about 1:8 was observed. Fluorescence spectroscopy of the same solutions with the subsequent correction of the recorded fluorescence intensity on the primary inner filter effect allowed us to determine another mode of ThT binding to fibrils, with a binding constant of about 106 M−1 and stoichiometry of about 1:2500. Analysis of the photophysical characteristics of the dye molecules bound to the sites of different binding modes allowed us to assume the possible localization of these sites. The obtained differences in the ThT binding parameters to the amyloid fibrils formed from α-synuclein and other amyloidogenic proteins, as well as in the photophysical characteristics of the bound dye, confirmed the hypothesis of amyloid fibril polymorphism.
Collapse
|
16
|
Spehar K, Ding T, Sun Y, Kedia N, Lu J, Nahass GR, Lew MD, Bieschke J. Super-resolution Imaging of Amyloid Structures over Extended Times by Using Transient Binding of Single Thioflavin T Molecules. Chembiochem 2018; 19:1944-1948. [PMID: 29953718 DOI: 10.1002/cbic.201800352] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 01/28/2023]
Abstract
Oligomeric amyloid structures are crucial therapeutic targets in Alzheimer's and other amyloid diseases. However, these oligomers are too small to be resolved by standard light microscopy. We have developed a simple and versatile tool to image amyloid structures by using thioflavin T without the need for covalent labeling or immunostaining. The dynamic binding of single dye molecules generates photon bursts that are used for fluorophore localization on a nanometer scale. Thus, photobleaching cannot degrade image quality, allowing for extended observation times. Super-resolution transient amyloid binding microscopy promises to directly image native amyloid by using standard probes and record amyloid dynamics over minutes to days. We imaged amyloid fibrils from multiple polypeptides, oligomeric, and fibrillar structures formed during different stages of amyloid-β aggregation, as well as the structural remodeling of amyloid-β fibrils by the compound epi-gallocatechin gallate.
Collapse
Affiliation(s)
- Kevin Spehar
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tianben Ding
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Yuanzi Sun
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.,Department of Energy, Environmental, and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Niraja Kedia
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Jin Lu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - George R Nahass
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Jan Bieschke
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.,MRC Prion Unit, UCL Institute of Prion Diseases, Gower Street, London, WC1E 6BT, UK
| |
Collapse
|
17
|
Sulatskaya AI, Rychkov GN, Sulatsky MI, Rodina NP, Kuznetsova IM, Turoverov KK. Thioflavin T Interaction with Acetylcholinesterase: New Evidence of 1:1 Binding Stoichiometry Obtained with Samples Prepared by Equilibrium Microdialysis. ACS Chem Neurosci 2018; 9:1793-1801. [PMID: 29652131 DOI: 10.1021/acschemneuro.8b00111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The aim of the present work was investigation of the fluorescent dye thioflavin T (ThT) binding to acetylcholinesterase (AChE). ThT is an effective test for protease activity, as well as a probe for amyloid fibril formation. Despite the extended and active investigation of ThT-AChE binding, there is still no common view on the stoichiometry of this interaction. In particular, there is a hypothesis explaining the spectral properties of bound to AChE dye and high quantum yield of its fluorescence by formation of dimers or excimers of ThT. In order to confirm or deny this hypothesis, we proposed a new experimental approach for examination of ThT-AChE interaction based on spectroscopic investigation of samples prepared by equilibrium microdialysis. This approach allowed us to prove 1/1 ThT/AChE binding stoichiometry. The increase of ThT fluorescence quantum yield and lifetime accompanying its binding to AChE can be explained by the molecular rotor nature of this dye. Together with the coincidence of the positions of free and AChE-bound ThT fluorescence spectra, the obtained results prove the groundlessness of the hypotheses about ThT aggregation while binding to AChE. The model of ThT localization in the active site of AChE was proposed by using molecular docking simulations. These results also allowed us to suggest the key role of aromatic residues in ThT-AChE interaction, as observed for some amyloid fibrils.
Collapse
Affiliation(s)
- A. 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
| | - G. N. Rychkov
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St.-Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russia
- Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Orlova Roscha, Gatchina, Leningrad District, 188300, Russia
| | - M. 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
| | - N. 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
- Institute of Physics, Nanotechnology and Telecommunications, Peter the Great St.-Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russia
| | - I. 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
| | - K. 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
| |
Collapse
|
18
|
Sundaram GSM, Binz K, Sharma V, Yeung M, Sharma V. Live-cell fluorescence imaging: assessment of thioflavin T uptake in human epidermal carcinoma cells. MEDCHEMCOMM 2018; 9:946-950. [PMID: 30108983 PMCID: PMC6072315 DOI: 10.1039/c8md00101d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/14/2018] [Indexed: 11/21/2022]
Abstract
Thioflavin T (ThT), a positively charged heterocyclic small molecule, is a widely used fluorescent marker of amyloid pathophysiology to confirm the cause of death in post mortem brain tissue of Alzheimer's disease (AD) patients. Literature precedents indicate that current positron emission tomography (PET) agents, such as 11C-PIB and 18F-flutemetamol, share significant structural similarity with ThT, a lipophilic dye which does not traverse the blood-brain barrier (BBB) to enable the detection of Aβ plaques in vivo. While vital for maintaining normal physiology and healthy brain function, the BBB comprises brain endothelial cells sealed via paracellular protein complexes, bound by an extracellular matrix forming tight junctions thus controlling the delivery of molecules into the brain. The human P-glycoprotein (Pgp/ABCB1, 170 kD plasma membrane protein), belonging to the ABC family of efflux transporter proteins, also lines the luminal surface of brain endothelial cells thus poised to secrete its recognized substrates into the blood. Herein, we postulate that thioflavin T (ThT), due to its physico-chemical attributes, such as moderate lipophilicity and protonated nitrogen, could very well be recognized as a transport substrate of Pgp (P-glycoprotein, ABCB1) thus restricting its permeation into the brain. To evaluate whether or not ThT is indeed recognized by Pgp as its transport substrate thus limiting its BBB permeability, herein, we evaluate cellular accumulation profiles of ThT and PiB (a similar structural uncharged mimetic) in human epidermal carcinoma KB-3-1 (Pgp-) and MDR KB-8-5 (Pgp+) cells, using live-cell fluorescence imaging. While ThT penetrates KB-3-1 cells, it gets excluded from KB-8-5 cells, and also indicates LY335979-induced uptake in Pgp-expressing cells. Furthermore, the cellular uptake profiles of PiB are not impacted by the expression of Pgp under identical conditions. These data show that uptake profiles of ThT have been modified by the expression of Pgp in these cells, and are inversely proportional to the expression of the transporter protein located on the plasma membrane of these cells. Combined data demonstrate that ThT is efficiently recognized by Pgp as its transport substrate.
Collapse
Affiliation(s)
- G S M Sundaram
- ICCE Institute , Molecular Imaging Center , Mallinckrodt Institute of Radiology , Washington University School of Medicine , St. Louis , MO 63110 , USA .
| | - Kristen Binz
- ICCE Institute , Molecular Imaging Center , Mallinckrodt Institute of Radiology , Washington University School of Medicine , St. Louis , MO 63110 , USA .
| | - Vedica Sharma
- ICCE Institute , Molecular Imaging Center , Mallinckrodt Institute of Radiology , Washington University School of Medicine , St. Louis , MO 63110 , USA .
| | - Melany Yeung
- Students and Teachers as Research Scientists (STARS) Program , USA
| | - Vijay Sharma
- ICCE Institute , Molecular Imaging Center , Mallinckrodt Institute of Radiology , Washington University School of Medicine , St. Louis , MO 63110 , USA .
- Students and Teachers as Research Scientists (STARS) Program , USA
- Department of Neurology , Washington University School of Medicine , St. Louis , MO 63110 , USA
- Department of Biomedical Engineering , School of Engineering & Applied Science , Washington University , St. Louis 63105 , USA
| |
Collapse
|
19
|
Identification of post-translational modifications of Aβ peptide in platelet membranes from patients with cerebral amyloid angiopathy. J Neurol Sci 2017; 383:11-17. [DOI: 10.1016/j.jns.2017.08.3269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/28/2017] [Accepted: 08/31/2017] [Indexed: 01/13/2023]
|
20
|
Peccati F, Pantaleone S, Riffet V, Solans-Monfort X, Contreras-García J, Guallar V, Sodupe M. Binding of Thioflavin T and Related Probes to Polymorphic Models of Amyloid-β Fibrils. J Phys Chem B 2017; 121:8926-8934. [DOI: 10.1021/acs.jpcb.7b06675] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Francesca Peccati
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Stefano Pantaleone
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vanessa Riffet
- Laboratoire
de Chimie Théorique (LCT), Sorbonne Universités, UPMC Univ Paris 06, CNRS, 4 place Jussieu, F-75005 Paris, France
- Institut Photovoltaïque d’Ile de France (IPVF), 8 rue de la Renaissance, 92160 Antony, France
- Institute for Research and Development of Photovoltaic Energy (IRDEP), UMR 7174 CNRS/EDF R&D/Chimie ParisTech-PSL, 6 quai Watier, 78401 Chatou, France
| | | | - Julia Contreras-García
- Laboratoire
de Chimie Théorique (LCT), Sorbonne Universités, UPMC Univ Paris 06, CNRS, 4 place Jussieu, F-75005 Paris, France
| | - Victor Guallar
- Joint
Barcelona Supercomputing Center - Centre for Genomic Regulation -
Institute for Research in Biomedicine - Research Program in Computational
Biology, Barcelona Supercomputing Center, Barcelona, Spain
- ICREA, Passeig Lluís
Companys 23, E-08010 Barcelona, Spain
| | - Mariona Sodupe
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- ICREA, Passeig Lluís
Companys 23, E-08010 Barcelona, Spain
| |
Collapse
|
21
|
Sulatskaya AI, Rodina NP, Povarova OI, Kuznetsova IM, Turoverov KK. Different conditions of fibrillogenesis cause polymorphism of lysozyme amyloid fibrils. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|