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Nabi Afjadi M, Aziziyan F, Farzam F, Dabirmanesh B. Biotechnological applications of amyloid fibrils. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:435-472. [PMID: 38811087 DOI: 10.1016/bs.pmbts.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Protein aggregates and amyloid fibrils have special qualities and are used in a variety of biotechnological applications. They are extensively employed in bioremediation, biomaterials, and biocatalysis. Because of their capacity to encapsulate and release pharmaceuticals and their sensitivity to certain molecules, respectively, they are also used in drug delivery and biosensor applications. They have also demonstrated potential in the domains of food and bioremediation. Additionally, amyloid peptides have drawn interest in biological applications, especially in the investigation of illnesses like Parkinson's and Alzheimer's. The unique characteristics of amyloid fibrils, namely their mechanical strength and β-sheet structure, make them adaptable to a wide range of biotechnological uses. Even with their promise, one important factor to keep in mind before widely using modified amyloid materials is their potential toxicity. Thus, current research aims to overcome safety concerns while maximizing their potential.
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Affiliation(s)
- Mohsen Nabi Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farnoosh Farzam
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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2
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Fitzner L, Hasler M, Heyn TR, Schwarz K, Keppler JK. UVB pretreatment of β-lactoglobulin affects the temperature-induced formation of functional amyloid-like aggregates and promotes oxidative degradation. Food Chem 2023; 429:136898. [PMID: 37516047 DOI: 10.1016/j.foodchem.2023.136898] [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: 03/17/2023] [Revised: 06/11/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
Unfolding in combination with or without acid hydrolysis is crucial for the formation of functional amyloid (fibrillar) or amyloid-like (worm-like) β-lactoglobulin (BLG) aggregates, which can be induced through temperature treatment for several hours at pH 2-4. A preceding conformational destabilization of BLG might affect its aggregation. We investigated ultraviolet (UV) B radiation as conformational perturbing treatment to facilitate temperature-induced protein aggregation. 2-h UVB pretreated BLG (UV-BLG) exhibited an accelerated worm-like aggregation at pH 3.5, while at pH 2 the formation of fibrils was decelerated. The UV-induced conformational destabilization lowered the thermal stability and thus facilitates unfolding during thermal treatment. Thereby, the formation of covalent and non-covalent intermolecular interactions was favored, which promoted assembly of intact proteins resulting in worm-like aggregates. The oxidative degradation of UV-BLG was suggested to alter fibrillation-prone protein regions and thereby impede peptide assembly.
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Affiliation(s)
- Laura Fitzner
- Institute of Human Nutrition and Food Science, Division Food Technology, Christian-Albrechts-University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany.
| | - Mario Hasler
- Lehrfach Variationsstatistik, Christian-Albrechts-University of Kiel, Hermann-Rodewald-Strasse 9, 24118 Kiel, Germany.
| | - Timon R Heyn
- Institute of Human Nutrition and Food Science, Division Food Technology, Christian-Albrechts-University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany.
| | - Karin Schwarz
- Institute of Human Nutrition and Food Science, Division Food Technology, Christian-Albrechts-University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany.
| | - Julia Katharina Keppler
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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3
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Hoppenreijs LJG, Overbeck A, Brune SE, Biedendieck R, Kwade A, Krull R, Boom RM, Keppler JK. Amyloid-like aggregation of recombinant β-lactoglobulin at pH 3.5 and 7.0: Is disulfide bond removal the key to fibrillation? Int J Biol Macromol 2023; 242:124855. [PMID: 37187417 DOI: 10.1016/j.ijbiomac.2023.124855] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/19/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Functional nanofibrils from globular proteins are usually formed by heating for several hours at pH 2.0, which induces acidic hydrolysis and consecutive self-association. The functional properties of these micro-metre-long anisotropic structures are promising for biodegradable biomaterials and food applications, but their stability at pH > 2.0 is low. The results presented here show that modified β-lactoglobulin can also form nanofibrils by heating at neutral pH without prior acidic hydrolysis; the key is removing covalent disulfide bonds. The aggregation behaviour of various recombinant β-lactoglobulin variants was systemically studied at pH 3.5 and 7.0. The suppression of intra- and intermolecular disulfide bonds by eliminating one to three out of the five cysteines makes the non-covalent interactions more prevalent and allow for structural rearrangement. This stimulated the linear growth of worm-like aggregates. Full elimination of all five cysteines led to the transformation of worm-like aggregates into actual fibril structures (several hundreds of nanometres long) at pH 7.0. This understanding of the role of cysteine in protein-protein interactions will help to identify proteins and protein modifications to form functional aggregates at neutral pH.
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Affiliation(s)
- Loes J G Hoppenreijs
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Achim Overbeck
- Technische Universität Braunschweig, Institute of Particle Technology, Volkmaroderstrasse 5, 38104 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Sarah E Brune
- Technische Universität Braunschweig, Institute of Biochemical Engineering, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Institute of Microbiology, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Rebekka Biedendieck
- Technische Universität Braunschweig, Institute of Microbiology, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany
| | - Arno Kwade
- Technische Universität Braunschweig, Institute of Particle Technology, Volkmaroderstrasse 5, 38104 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Rainer Krull
- Technische Universität Braunschweig, Institute of Biochemical Engineering, Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106 Braunschweig, Germany; Technische Universität Braunschweig, Center of Pharmaceutical Engineering (PVZ), Franz-Liszt-Straße 35a, 38106 Braunschweig, Germany
| | - Remko M Boom
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Julia K Keppler
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
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Hoppenreijs LJ, Brune SE, Biedendieck R, Krull R, Boom RM, Keppler JK. Fibrillation of β-lactoglobulin at pH 2.0: Impact of cysteine substitution and disulfide bond reduction intended for food Hydrocolloids. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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5
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Wen H, Li J, Zhang Q, Inose T, Peeters W, Fortuni B, Asakawa H, Masuhara A, Hirai K, Toyouchi S, Fujita Y, Uji-I H. Length-Controllable Gold-Coated Silver Nanowire Probes for High AFM-TERS Scattering Activity. NANO LETTERS 2023; 23:1615-1621. [PMID: 36484776 DOI: 10.1021/acs.nanolett.2c03985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Tip-enhanced Raman scattering (TERS) microscopy is an advanced technique for investigation at the nanoscale that provides topographic and chemical information simultaneously. The TERS probe plays a crucial role in the microscopic performance. In the recent past, the development of silver nanowire (AgNW) based TERS probes solved the main tip fabrication issues, such as low mechanical strength and reproducibility. However, this fabrication method still suffers from low control of the protruded length of the AgNW. In this work, a simple water-air interface electrocutting method is proposed to achieve wide controllability of the length. This water cutting method was combined with a succedent Au coating on the AgNW surface, and the probe achieved an up to 100× higher enhancement factor (EF) and a 2× smaller spatial resolution compared to pristine AgNW. Thanks to this excellent EF, the water-cut Au-coated AgNW probes were found to possess high TERS activity even in the nongap mode, enabling broad applications.
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Affiliation(s)
- Han Wen
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan
| | - Jiangtao Li
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan
| | - Qiang Zhang
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan
| | - Tomoko Inose
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
| | - Wannes Peeters
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Beatrice Fortuni
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Hitoshi Asakawa
- Nanomaterials Research Institute (NanoMaRi), Graduate School of Natural Science and Technology, and Nano Life Science Institute (NanoLSI), Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Akito Masuhara
- Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Kenji Hirai
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan
| | - Shuichi Toyouchi
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
- Department of Applied Chemistry, College of Science, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yasuhiko Fujita
- Toray Research Center, Inc., Sonoyama 3-3-7, Otsu, Shiga 520-8567, Japan
| | - Hiroshi Uji-I
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto, Kyoto 606-8501, Japan
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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6
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Heyn TR, Schrader M, Kampen I, Kwade A, Schwarz K, Keppler JK. Glass beads increase the formation kinetics of beta-lactoglobulin amyloid fibrils. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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7
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Jaklin M, Hritz J, Hribar-Lee B. A new fibrillization mechanism of β-lactoglobulin in glycine solutions. Int J Biol Macromol 2022; 216:414-425. [PMID: 35803407 PMCID: PMC10039397 DOI: 10.1016/j.ijbiomac.2022.06.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/15/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
Even though amyloid aggregates were discovered many years ago the mechanism of their formation is still a mystery. Because of their connection to many of untreatable neurodegenerative diseases the motivation for finding a common aggregation path is high. We report a new high heat induced fibrillization path of a model protein β-lactoglobulin (BLG) when incubated in glycine instead of water at pH 2. By combining atomic force microscopy (AFM), transmission emission microscopy (TEM), dynamic light scattering (DLS) and circular dichroism (CD) we predict that the basic building blocks of fibrils made in glycine are not peptides, but rather spheroid oligomers of different height that form by stacking of ring-like structures. Spheroid oligomers linearly align to form fibrils by opening up and combining. We suspect that glycine acts as an hydrolysation inhibitor which consequently promotes a different fibrillization path. By combining the known data on fibrillization in water with our experimental conclusions we come up with a new fibrillization scheme for BLG. We show that by changing the fibrillization conditions just by small changes in buffer composition can dramatically change the aggregation pathway and the effect of buffer shouldn't be neglected. Fibrils seen in our study are also gaining more and more attention because of their pore-like structure and a possible cytotoxic mechanism by forming pernicious ion-channels. By preparing them in a simple model system as BLG we opened a new way to study their formation.
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Affiliation(s)
- Matej Jaklin
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Jozef Hritz
- CEITEC Masaryk University Kamenice 5, Brno 625 00, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University Kamenice 5, Brno 625 00, Czech Republic
| | - Barbara Hribar-Lee
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia.
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8
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Wen H, Inose T, Hirai K, Akashi T, Sugioka S, Li J, Peeters W, Fron E, Fortuni B, Nakata Y, Rocha S, Toyouchi S, Fujita Y, Uji-I H. Gold-coated silver nanowires for long lifetime AFM-TERS probes. NANOSCALE 2022; 14:5439-5446. [PMID: 35322821 DOI: 10.1039/d1nr07833j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tip-enhanced Raman scattering (TERS) microscopy is an advanced technique for investigation at the nanoscale because of its excellent properties, such as its label-free functionality, non-invasiveness, and ability to simultaneously provide topographic and chemical information. The probe plays a crucial role in TERS technique performance. Widely used AFM-TERS probes fabricated with metal deposition suffer from relatively low reproductivity as well as limited mapping and storage lifetime. To solve the reproducibility issue, silver nanowire (AgNW)-based TERS probes were developed, which, thanks to the high homogeneity of the liquid-phase synthesis of AgNW, can achieve high TERS performance with excellent probe reproductivity, but still present short lifetime due to probe oxidation. In this work, a simple Au coating method is proposed to overcome the limited lifetime and improve the performance of the AgNW-based TERS probe. For the Au-coating, different [Au]/[Ag] molar ratios were investigated. The TERS performance was evaluated in terms of changes in the enhancement factor (EF) and signal-to-noise ratio through multiple mappings and the storage lifetime in air. The Au-coated AgNWs exhibited higher EF than pristine AgNWs and galvanically replaced AgNWs with no remarkable difference between the two molar ratios tested. However, for longer scanning time and multiple mappings, the probes obtained with low Au concentration showed much longer-term stability and maintained a high EF. Furthermore, the Au-coated AgNW probes were found to possess a longer storage lifetime in air, allowing for long and multiple TERS mappings with one single probe.
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Affiliation(s)
- Han Wen
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan.
| | - Tomoko Inose
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kenji Hirai
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan.
| | - Taiki Akashi
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan.
| | - Shoji Sugioka
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan.
| | - Jiangtao Li
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan.
| | - Wannes Peeters
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Eduard Fron
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Beatrice Fortuni
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Yoshihiko Nakata
- Toray Research Center, Inc., Sonoyama 3-3-7, Otsu 520-8567, Shiga, Japan
| | - Susana Rocha
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Shuichi Toyouchi
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Yasuhiko Fujita
- Toray Research Center, Inc., Sonoyama 3-3-7, Otsu 520-8567, Shiga, Japan
| | - Hiroshi Uji-I
- Research Institute for Electronic Science (RIES) and Division of Information Science and Technology, Graduate School of Information Science and Technology, Hokkaido University, N20W10, Sapporo, Hokkaido 001-0020, Japan.
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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9
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Hoppenreijs L, Fitzner L, Ruhmlieb T, Heyn T, Schild K, van der Goot AJ, Boom R, Steffen-Heins A, Schwarz K, Keppler J. Engineering amyloid and amyloid-like morphologies of β-lactoglobulin. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107301] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Tiwari D, Singh VK, Baral B, Pathak DK, Jayabalan J, Kumar R, Tapryal S, Jha HC. Indication of Neurodegenerative Cascade Initiation by Amyloid-like Aggregate-Forming EBV Proteins and Peptide in Alzheimer's Disease. ACS Chem Neurosci 2021; 12:3957-3967. [PMID: 34609141 DOI: 10.1021/acschemneuro.1c00584] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The neurotropic potential of the Epstein-Barr virus (EBV) was demonstrated quite recently; however, the mechanistic details are yet to be explored. Therefore, the effects of EBV infection in the neural milieu remain underexplored. Previous reports have suggested the potential role of virus-derived peptides in seeding the amyloid-β aggregation cascade, which lies at the center of Alzheimer's disease (AD) pathophysiology. However, no such study has been undertaken to explore the role of EBV peptides in AD. In our research, ∼100 EBV proteins were analyzed for their aggregation proclivity in silico using bioinformatic tools, followed by the prediction of 20S proteasomal cleavage sites using online algorithms NetChop ver. 3.1 and Pcleavage, thereby mimicking the cellular proteasomal cleavage activity generating short antigenic peptides of viral origin. Our study reports a high aggregate-forming tendency of a 12-amino-acid-long (146SYKHVFLSAFVY157) peptide derived from EBV glycoprotein M (EBV-gM). The in vitro analysis of aggregate formation done using Congo red and Thioflavin-S assays demonstrated dose- and time-dependent kinetics. Thereafter, Raman spectroscopy was used to validate the formation of secondary structures (α helix, β sheets) in the aggregates. Additionally, cytotoxicity assay revealed that even a low concentration of these aggregates has a lethal effect on neuroblastoma cells. The findings of this study provide insights into the mechanistic role of EBV in AD and open up new avenues to explore in the future.
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Affiliation(s)
- Deeksha Tiwari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Vikas Kumar Singh
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Budhadev Baral
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Devesh Kumar Pathak
- Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Jesumony Jayabalan
- Nano Science Laboratory, MSS, Raja Ramanna Centre for Advanced Technology, Indore 452013, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Rajesh Kumar
- Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
- Centre for Advanced Electronics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Suman Tapryal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
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11
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Nguyen H, Linh HQ, Matteini P, La Penna G, Li MS. Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study. J Phys Chem B 2020; 124:10617-10631. [PMID: 33180492 PMCID: PMC7735726 DOI: 10.1021/acs.jpcb.0c05508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/29/2020] [Indexed: 12/20/2022]
Abstract
Amyloid-β (Aβ) peptides form assemblies that are pathological hallmarks of Alzheimer's disease. Aβ oligomers are soluble, mobile, and toxic forms of the peptide that act in the extracellular space before assembling into protofibrils and fibrils. Therefore, oligomers play an important role in the mechanism of Alzheimer's disease. Since it is difficult to determine by experiment the atomic structures of oligomers, which accumulate fast and are polymorphic, computer simulation is a useful tool to investigate elusive oligomers' structures. In this work, we report extended all-atom molecular dynamics simulations, both canonical and replica exchange, of Aβ(1-42) trimer starting from two different initial conformations: (i) the pose produced by the best docking of a monomer aside of a dimer (simulation 1), representing oligomers freshly formed by assembling monomers, and (ii) a configuration extracted from an experimental mature fibril structure (simulation 2), representing settled oligomers in equilibrium with extended fibrils. We showed that in simulation 1, regions with small β-barrels are populated, indicating the chance of spontaneous formation of domains resembling channel-like structures. These structural domains are alternative to those more representative of mature fibrils (simulation 2), the latter showing a stable bundle of C-termini that is not sampled in simulation 1. Moreover, trimer of Aβ(1-42) can form internal pores that are large enough to be accessed by water molecules and Ca2+ ions.
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Affiliation(s)
- Hoang
Linh Nguyen
- Institute
for Computational Science and Technology, SBI Building, Quang Trung Software
City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Huynh Quang Linh
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Paolo Matteini
- Institute
of Applied Physics “Nello Carrara”, National Research Council, Via Madonna Del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - Giovanni La Penna
- National
Research Council of Italy (CNR), Institute
for Chemistry of Organometallic Compounds (ICCOM), 50019 Florence, Italy
- National Institute for Nuclear Physics
(INFN), Section of Roma-Tor
Vergata Institute of Physics, Polish Academy of
Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- National Institute for Nuclear Physics
(INFN), Section of Roma-Tor
Vergata Institute of Physics, Polish Academy of
Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
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12
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Kayser JJ, Arnold P, Steffen-Heins A, Schwarz K, Keppler JK. Functional ethanol-induced fibrils: Influence of solvents and temperature on amyloid-like aggregation of beta-lactoglobulin. J FOOD ENG 2020. [DOI: 10.1016/j.jfoodeng.2019.109764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Banchelli M, Cascella R, D'Andrea C, Cabaj L, Osticioli I, Ciofini D, Li MS, Skupień K, de Angelis M, Siano S, Cecchi C, Pini R, La Penna G, Chiti F, Matteini P. Nanoscopic insights into the surface conformation of neurotoxic amyloid β oligomers. RSC Adv 2020; 10:21907-21913. [PMID: 35516647 PMCID: PMC9054531 DOI: 10.1039/d0ra03799k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/01/2020] [Indexed: 11/21/2022] Open
Abstract
Raman spectroscopy assisted by localized plasmon resonances generating effective hot spots at the gaps between intertwined silver nanowires is herein adopted to unravel characteristic molecular motifs on the surface of Aβ42 misfolded oligomers that are critical in driving intermolecular interactions in neurodegeneration. Unraveling characteristic structural determinants at the basis of Aβ42 oligomers' neurotoxicity by a sub-molecular SERS investigation of their surface.![]()
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14
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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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15
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Protein Microgels from Amyloid Fibril Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:223-263. [PMID: 31713201 DOI: 10.1007/978-981-13-9791-2_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Nanofibrillar forms of amyloidogenic proteins were initially discovered in the context of protein misfolding and disease but have more recently been found at the origin of key biological functionality in many naturally occurring functional materials, such as adhesives and biofilm coatings. Their physiological roles in nature reflect their great strength and stability, which has led to the exploration of their use as the basis of artificial protein-based functional materials. Particularly for biomedical applications, they represent attractive building blocks for the development of, for instance, drug carrier agents due to their inherent biocompatibility and biodegradability. Furthermore, the propensity of proteins to self-assemble into amyloid fibrils can be exploited under microconfinement, afforded by droplet microfluidic techniques. This approach allows the generation of multi-scale functional microgels that can host biological additives and can be designed to incorporate additional functionality, such as to aid targeted drug delivery.
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16
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Heyn TR, Garamus VM, Neumann HR, Uttinger MJ, Guckeisen T, Heuer M, Selhuber-Unkel C, Peukert W, Keppler JK. Influence of the polydispersity of pH 2 and pH 3.5 beta-lactoglobulin amyloid fibril solutions on analytical methods. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.08.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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17
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Bruzas I, Lum W, Gorunmez Z, Sagle L. Advances in surface-enhanced Raman spectroscopy (SERS) substrates for lipid and protein characterization: sensing and beyond. Analyst 2019; 143:3990-4008. [PMID: 30059080 DOI: 10.1039/c8an00606g] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) has become an essential ultrasensitive analytical tool for biomolecular analysis of small molecules, macromolecular proteins, and even cells. SERS enables label-free, direct detection of molecules through their intrinsic Raman fingerprint. In particular, protein and lipid bilayers are dynamic three-dimensional structures that necessitate label-free methods of characterization. Beyond direct detection and quantitation, the structural information contained in SERS spectra also enables deeper biophysical characterization of biomolecules near metallic surfaces. Therefore, SERS offers enormous potential for such systems, although making measurements in a nonperturbative manner that captures the full range of interactions and activity remains a challenge. Many of these challenges have been overcome through advances in SERS substrate development, which have expanded the applications and targets of SERS for direct biomolecular quantitation and biophysical characterization. In this review, we will first discuss different categories of SERS substrates including solution-phase, solid-supported, tip-enhanced Raman spectroscopy (TERS), and single-molecule substrates for biomolecular analysis. We then discuss detection of protein and biological lipid membranes. Lastly, biophysical insights into proteins, lipids and live cells gained through SERS measurements of these systems are reviewed.
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Affiliation(s)
- Ian Bruzas
- Department of Chemistry, University of Cincinnati, 301 Clifton Court, Cincinnati, OH 45221, USA.
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18
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Xu T, Langouras C, Koudehi MA, Vos BE, Wang N, Koenderink GH, Huang X, Vavylonis D. Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX. Sci Rep 2019; 9:1717. [PMID: 30737416 PMCID: PMC6368602 DOI: 10.1038/s41598-018-37182-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/03/2018] [Indexed: 01/03/2023] Open
Abstract
Studies of how individual semi-flexible biopolymers and their network assemblies change over time reveal dynamical and mechanical properties important to the understanding of their function in tissues and living cells. Automatic tracking of biopolymer networks from fluorescence microscopy time-lapse sequences facilitates such quantitative studies. We present an open source software tool that combines a global and local correspondence algorithm to track biopolymer networks in 2D and 3D, using stretching open active contours. We demonstrate its application in fully automated tracking of elongating and intersecting actin filaments, detection of loop formation and constriction of tilted contractile rings in live cells, and tracking of network deformation under shear deformation.
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Affiliation(s)
- Ting Xu
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA, 18015, USA
| | | | | | - Bart E Vos
- AMOLF, Living Matter Department, 1098 XG, Amsterdam, The Netherlands
| | - Ning Wang
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Xiaolei Huang
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA, 18015, USA.
- College of Information Sciences and Technology, Penn State University, University Park, PA, 16802, USA.
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19
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018; 57:8519-8524. [DOI: 10.1002/anie.201803234] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/22/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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20
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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21
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Deckert-Gaudig T, Taguchi A, Kawata S, Deckert V. Tip-enhanced Raman spectroscopy - from early developments to recent advances. Chem Soc Rev 2018. [PMID: 28640306 DOI: 10.1039/c7cs00209b] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An analytical technique operating at the nanoscale must be flexible regarding variable experimental conditions while ideally also being highly specific, extremely sensitive, and spatially confined. In this respect, tip-enhanced Raman scattering (TERS) has been demonstrated to be ideally suited to, e.g., elucidating chemical reaction mechanisms, determining the distribution of components and identifying and localizing specific molecular structures at the nanometre scale. TERS combines the specificity of Raman spectroscopy with the high spatial resolution of scanning probe microscopies by utilizing plasmonic nanostructures to confine the incident electromagnetic field and increase it by many orders of magnitude. Consequently, molecular structure information in the optical near field that is inaccessible to other optical microscopy methods can be obtained. In this general review, the development of this still-young technique, from early experiments to recent achievements concerning inorganic, organic, and biological materials, is addressed. Accordingly, the technical developments necessary for stable and reliable AFM- and STM-based TERS experiments, together with the specific properties of the instruments under different conditions, are reviewed. The review also highlights selected experiments illustrating the capabilities of this emerging technique, the number of users of which has steadily increased since its inception in 2000. Finally, an assessment of the frontiers and new concepts of TERS, which aim towards rendering it a general and widely applicable technique that combines the highest possible lateral resolution and extreme sensitivity, is provided.
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22
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Affiliation(s)
- Lifu Xiao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Zachary D Schultz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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23
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Bonhommeau S, Lecomte S. Tip-Enhanced Raman Spectroscopy: A Tool for Nanoscale Chemical and Structural Characterization of Biomolecules. Chemphyschem 2017; 19:8-18. [DOI: 10.1002/cphc.201701067] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Sébastien Bonhommeau
- University of Bordeaux; Institut des Sciences Moléculaires; CNRS UMR 5255; 351 cours de la Libération 33405 Talence cedex France
| | - Sophie Lecomte
- University of Bordeaux; Institut de Chimie et Biologie des Membranes et des Nano-objets; CNRS UMR 5248; Allée Geoffroy Saint Hilaire 33600 Pessac France
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24
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Khan JM, Khan MS, Qadeer A, Alsenaidy MA, Ahmed A, Al-Shabib NA, Khan RH. Cationic gemini surfactant (16-4-16) interact electrostatically with anionic plant lectin and facilitates amyloid fibril formation at neutral pH. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2017.03.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Bonhommeau S, Talaga D, Hunel J, Cullin C, Lecomte S. Tip-Enhanced Raman Spectroscopy to Distinguish Toxic Oligomers from Aβ1-
42
Fibrils at the Nanometer Scale. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610399] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sébastien Bonhommeau
- University of Bordeaux; Institut des Sciences Moléculaires, CNRS UMR 5255; 351 cours de la Libération 33405 Talence cedex France
| | - David Talaga
- University of Bordeaux; Institut des Sciences Moléculaires, CNRS UMR 5255; 351 cours de la Libération 33405 Talence cedex France
| | - Julien Hunel
- University of Bordeaux; Institut des Sciences Moléculaires, CNRS UMR 5255; 351 cours de la Libération 33405 Talence cedex France
| | - Christophe Cullin
- University of Bordeaux; Institut de Chimie et Biologie des Membranes et des Nano-objets, CNRS UMR 5248; Allée Geoffroy Saint Hilaire 33600 Pessac France
| | - Sophie Lecomte
- University of Bordeaux; Institut de Chimie et Biologie des Membranes et des Nano-objets, CNRS UMR 5248; Allée Geoffroy Saint Hilaire 33600 Pessac France
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26
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Bonhommeau S, Talaga D, Hunel J, Cullin C, Lecomte S. Tip-Enhanced Raman Spectroscopy to Distinguish Toxic Oligomers from Aβ 1-42 Fibrils at the Nanometer Scale. Angew Chem Int Ed Engl 2017; 56:1771-1774. [PMID: 28071842 DOI: 10.1002/anie.201610399] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/02/2016] [Indexed: 11/09/2022]
Abstract
For the first time, natural Aβ1-42 fibrils (WT) implicated in Alzheimer's disease, as well as two synthetic mutants forming less toxic amyloid fibrils (L34T) and highly toxic oligomers (oG37C), are chemically characterized at the scale of a single structure using tip-enhanced Raman spectroscopy (TERS). While the proportion of TERS features associated with amino acid residues is similar for the three peptides, a careful examination of amide I and amide III bands allows us to clearly distinguish WT and L34T fibers organized in parallel β-sheets from the small and more toxic oG37C oligomers organized in anti-parallel β-sheets.
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Affiliation(s)
- Sébastien Bonhommeau
- University of Bordeaux, Institut des Sciences Moléculaires, CNRS UMR 5255, 351 cours de la Libération, 33405, Talence cedex, France
| | - David Talaga
- University of Bordeaux, Institut des Sciences Moléculaires, CNRS UMR 5255, 351 cours de la Libération, 33405, Talence cedex, France
| | - Julien Hunel
- University of Bordeaux, Institut des Sciences Moléculaires, CNRS UMR 5255, 351 cours de la Libération, 33405, Talence cedex, France
| | - Christophe Cullin
- University of Bordeaux, Institut de Chimie et Biologie des Membranes et des Nano-objets, CNRS UMR 5248, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
| | - Sophie Lecomte
- University of Bordeaux, Institut de Chimie et Biologie des Membranes et des Nano-objets, CNRS UMR 5248, Allée Geoffroy Saint Hilaire, 33600, Pessac, France
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27
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Gong G, Wang W, Du W. Binuclear ruthenium complexes inhibit the fibril formation of human islet amyloid polypeptide. RSC Adv 2017. [DOI: 10.1039/c6ra28107a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Binuclear ruthenium complexes reverse the aggregation of human islet amyloid polypeptide.
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Affiliation(s)
- Gehui Gong
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Wenji Wang
- Department of Chemistry
- Renmin University of China
- Beijing
- China
| | - Weihong Du
- Department of Chemistry
- Renmin University of China
- Beijing
- China
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