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Polańska O, Szulc N, Stottko R, Olek M, Nadwodna J, Gąsior-Głogowska M, Szefczyk M. Challenges in Peptide Solubilization - Amyloids Case Study. CHEM REC 2024:e202400053. [PMID: 39023378 DOI: 10.1002/tcr.202400053] [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: 03/18/2024] [Revised: 05/23/2024] [Indexed: 07/20/2024]
Abstract
Peptide science has been a rapidly growing research field because of the enormous potential application of these biocompatible and bioactive molecules. However, many factors limit the widespread use of peptides in medicine, and low solubility is among the most common problems that hamper drug development in the early stages of research. Solubility is a crucial, albeit poorly understood, feature that determines peptide behavior. Several different solubility predictors have been proposed, and many strategies and protocols have been reported to dissolve peptides, but none of them is a one-size-fits-all method for solubilization of even the same peptide. In this review, we look for the reasons behind the difficulties in dissolving peptides, analyze the factors influencing peptide aggregation, conduct a critical analysis of solubilization strategies and protocols available in the literature, and give some tips on how to deal with the so-called difficult sequences. We focus on amyloids, which are particularly difficult to dissolve and handle such as amyloid beta (Aβ), insulin, and phenol-soluble modulins (PSMs).
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Affiliation(s)
- Oliwia Polańska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Natalia Szulc
- Department of Physics and Biophysics, Wroclaw University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
| | - Rafał Stottko
- Faculty of Chemistry, Wrocław University of Science and Technology, Gdanska 7/9, 50-344, Wrocław, Poland
| | - Mateusz Olek
- Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Traugutta 2, 41-800 Zabrze, Poland
| | - Julita Nadwodna
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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Yuzu K, Imamura H, Nozaki T, Fujii Y, Badawy SMM, Morishima K, Okuda A, Inoue R, Sugiyama M, Chatani E. Mechanistic Modeling of Amyloid Oligomer and Protofibril Formation in Bovine Insulin. J Mol Biol 2024; 436:168461. [PMID: 38301805 DOI: 10.1016/j.jmb.2024.168461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Early phase of amyloid formation, where prefibrillar aggregates such as oligomers and protofibrils are often observed, is crucial for understanding pathogenesis. However, the detailed mechanisms of their formation have been difficult to elucidate because they tend to form transiently and heterogeneously. Here, we found that bovine insulin protofibril formation proceeds in a monodisperse manner, which allowed us to characterize the detailed early aggregation process by light scattering in combination with thioflavin T fluorescence and Fourier transform infrared spectroscopy. The protofibril formation was specific to bovine insulin, whereas no significant aggregation was observed in human insulin. The kinetic analysis combining static and dynamic light scattering data revealed that the protofibril formation process in bovine insulin can be divided into two steps based on fractal dimension. When modeling the experimental data based on Smoluchowski aggregation kinetics, an aggregation scheme consisting of initial fractal aggregation forming spherical oligomers and their subsequent end-to-end association forming protofibrils was clarified. Furthermore, the analysis of temperature and salt concentration dependencies showed that the end-to-end association is the rate-limiting step, involving dehydration. The established model for protofibril formation, wherein oligomers are incorporated as a precursor, provides insight into the molecular mechanism by which protein molecules assemble during the early stage of amyloid formation.
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Affiliation(s)
- Keisuke Yuzu
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Hiroshi Imamura
- Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Takuro Nozaki
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Yuki Fujii
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Shaymaa Mohamed Mohamed Badawy
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan; Department of Agricultural Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan.
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Maekawa S, Yuzu K, Chatani E, Morigaki K. Oligomerization and aggregation of NAP-22 with several metal ions. Neurosci Lett 2024; 821:137623. [PMID: 38184017 DOI: 10.1016/j.neulet.2023.137623] [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: 12/01/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024]
Abstract
Metal ions participate in various biochemical processes such as electron transport chain, gene transcription, and enzymatic reactions. Furthermore, the aggregation promoting effect of several metal ions on neuronal proteins such as prion, tau, Aβ peptide, and α-synuclein, has been reported. NAP-22 (also called BASP1 or CAP-23) is a neuron-enriched calmodulin-binding protein and one of the major proteins in the detergent-resistant membrane microdomain fraction of the neuronal cell membrane. Previously, we showed oligomer formation of NAP-22 in the presence of several phospholipids and fatty acids. In this study, we found the aggregation of NAP-22 by FeCl2, FeCl3, and AlCl3 using native-PAGE. Oligomer or aggregate formation of NAP-22 by ZnCl2 or CuSO4 was shown with SDS-PAGE after cross-linking with glutaraldehyde. Morphological analysis with electron microscopy revealed the formation of large aggregates composed of small annular oligomers in the presence of FeCl3, AlCl3, or CuSO4. In case of FeCl2 or ZnCl2, instead of large aggregates, scattered annular and globular oligomers were observed. Interestingly, metal ion induced aggregation of NAP-22 was inhibited by several coenzymes such as NADP+, NADPH, or thiamine pyrophosphate. Since NAP-22 is highly expressed in the presynaptic region of the synapse, this result suggests the participation of metal ions not only on the protein and membrane dynamics at the presynaptic region, but also on the metabolic regulation though the interaction with coenzymes.
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Affiliation(s)
- Shohei Maekawa
- Graduate School of Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501, Japan.
| | - Keisuke Yuzu
- Graduate School of Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501, Japan
| | - Kenichi Morigaki
- Graduate School of Agricultural Science, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501, Japan; Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501, Japan
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Yamamoto N, Inoue R, Makino Y, Sekiguchi H, Shibayama N, Naito A, Sugiyama M, Chatani E. Tracking the Structural Development of Amyloid Precursors in the Insulin B Chain and the Inhibition Effect by Fibrinogen. J Phys Chem B 2022; 126:10797-10812. [PMID: 36534755 DOI: 10.1021/acs.jpcb.2c05136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid fibrils are abnormal protein aggregates associated with several amyloidoses and neurodegenerative diseases. Prefibrillar intermediates, which emerge before amyloid fibril formation, play an important role in structure formation. Therefore, to prevent fibril formation, the mechanisms underpinning the structural development of prefibrillar intermediates must be elucidated. An insulin-derived peptide, the insulin B chain, is known for its stable accumulation of prefibrillar intermediates. In this study, the structural development of B chain prefibrillar intermediates and their inhibition by fibrinogen (Fg) were monitored by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) combined with solid-state nuclear magnetic resonance spectroscopy (NMR) and size exclusion chromatography. TEM images obtained in a time-lapse manner demonstrated that prefibrillar intermediates were wavy rod-like structures emerging from initial non-rod-like aggregates, and their bundling was responsible for protofilament formation. Time-resolved SAXS revealed that the prefibrillar intermediates became thicker and longer as a function of time. Solid-state NMR measurement suggested a β-sheet formation around Ala14 residue was crucial for the structural conversion from prefibrillar intermediates to amyloid fibril. These observations suggested that prefibrillar intermediates serve as reaction fields for amyloid nucleation and its structural propagation. Time-resolved SAXS also demonstrated that Fg prevented elongation of the prefibrillar intermediates by forming specific complexes together, which implied that regulation of the length of prefibrillar intermediates upon Fg binding was the factor suppressing the prefibrillar intermediate elongation. The fibril formation mechanism and the inhibition strategy found in this study will be helpful in seeking appropriate methods against amyloid-related diseases.
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Affiliation(s)
- Naoki Yamamoto
- Division of Biophysics, Physiology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi329-0498, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun, Osaka590-0494, Japan
| | - Yoshiteru Makino
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hotogaya-ku, Yokohama240-8501, Japan
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, 1-1-1, Koto, Sayo-cho, Sayo-gun, Hyogo679-5148, Japan
| | - Naoya Shibayama
- Division of Biophysics, Physiology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi329-0498, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hotogaya-ku, Yokohama240-8501, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun, Osaka590-0494, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe657-8501, Japan
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Watanabe-Nakayama T, Ono K. Single-molecule Observation of Self-Propagating Amyloid Fibrils. Microscopy (Oxf) 2022; 71:133-141. [DOI: 10.1093/jmicro/dfac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
The assembly of misfolded proteins into amyloid fibrils is associated with amyloidosis, including neurodegenerative diseases, such as Alzheimer’s, Parkinson’s, and prion diseases. The self-propagation of amyloid fibrils is widely observed in the aggregation pathways of numerous amyloidogenic proteins. This propensity with plasticity in primary nucleation allows amyloid fibril polymorphism, which is correlated with the pathology/phenotypes of patients. Because the interference with the nucleation and replication processes of amyloid fibrils can alter the amyloid structure and the outcome of the disease, these processes can be a target for developing clinical drugs. Single-molecule observation of amyloid fibril replication can be an experimental system to provide the kinetic parameters for simulation studies and confirm the effect of clinical drugs. Here, we review single-molecule observation of the amyloid fibril replication process using fluorescence microscopy and time-lapse atomic force microscopy, including high-speed atomic force microscopy. We discussed the amyloid fibril replication process and combined single-molecule observation results with molecular dynamics simulations.
Mini Abstract Structural dynamics in amyloid aggregation is related with various Alzheimer’s and Parkinson’s disease symptoms. Single-molecule observation using high-speed atomic force microscopy can directly visualize the structural dynamics of individual amyloid aggregate assemblies. Here, we review historical and recent studies of single-molecule observation of amyloid aggregation with supportive molecular dynamics simulation.
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Affiliation(s)
| | - Kenjiro Ono
- Department of Neurology and Neurobiology of Aging, Kanazawa University Graduate School of Medical Sciences, Kanazawa University, 13-1, Takara-machi, Kanazawa 920-8640, Japan
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