1
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Vugmeyster L, Au DF, Frazier B, Qiang W, Ostrovsky D. Rigidifying of the internal dynamics of amyloid-beta fibrils generated in the presence of synaptic plasma vesicles. Phys Chem Chem Phys 2024; 26:5466-5478. [PMID: 38277177 PMCID: PMC10956644 DOI: 10.1039/d3cp04824a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigated the changes in internal flexibility of amyloid-β1-40 (Aβ) fibrils grown in the presence of rat synaptic plasma vesicles. The fibrils are produced using a modified seeded growth protocol, in which the Aβ concentration is progressively increased at the expense of the decreased lipid to protein ratio. The morphologies of each generation are carefully assessed at several fibrils' growth time points using transmission electron microscopy. The side-chain dynamics in the fibrils is investigated using deuterium solid-state NMR measurements, with techniques spanning line shapes analysis and several NMR relaxation rates measurements. The dynamics is probed in the site-specific fashion in the hydrophobic C-terminal domain and the disordered N-terminal domain. An overall strong rigidifying effect is observed in comparison with the wild-type fibrils generated in the absence of the membranes. In particular, the overall large-scale fluctuations of the N-terminal domain are significantly reduced, and the activation energies of rotameric inter-conversion in methyl-bearing side-chains of the core (L17, L34, M35, V36), as well as the ring-flipping motions of F19 are increased, indicating a restricted core environment. Membrane-induced flexibility changes in Aβ aggregates can be important for the re-alignment of protein aggregates within the membrane, which in turn would act as a disruption pathway of the bilayers' integrity.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Bailey Frazier
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York, USA, 13902
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, USA, 80204
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2
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Liu H, Cui Y, Zhao X, Wei L, Wang X, Shen N, Odom T, Li X, Lawless W, Karunarathne K, Muschol M, Guida W, Cao C, Ye L, Cai J. Helical sulfonyl-γ-AApeptides modulating Aβ oligomerization and cytotoxicity by recognizing Aβ helix. Proc Natl Acad Sci U S A 2024; 121:e2311733121. [PMID: 38285951 PMCID: PMC10861862 DOI: 10.1073/pnas.2311733121] [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: 07/11/2023] [Accepted: 12/10/2023] [Indexed: 01/31/2024] Open
Abstract
In contrast to prevalent strategies which make use of β-sheet mimetics to block Aβ fibrillar growth, in this study, we designed a series of sulfonyl-γ-AApeptide helices that targeted the crucial α-helix domain of Aβ13-26 and stabilized Aβ conformation to avoid forming the neurotoxic Aβ oligomeric β-sheets. Biophysical assays such as amyloid kinetics and TEM demonstrated that the Aβ oligomerization and fibrillation could be greatly prevented and even reversed in the presence of sulfonyl-γ-AApeptides in a sequence-specific and dose-dependent manner. The studies based on circular dichroism, Two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) spectra unambiguously suggested that the sulfonyl-γ-AApeptide Ab-6 could bind to the central region of Aβ42 and induce α-helix conformation in Aβ. Additionally, Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) was employed to rule out a colloidal mechanism of inhibitor and clearly supported the capability of Ab-6 for inhibiting the formation of Aβ aggregated forms. Furthermore, Ab-6 could rescue neuroblastoma cells by eradicating Aβ-mediated cytotoxicity even in the presence of pre-formed Aβ aggregates. The confocal microscopy demonstrated that Ab-6 could still specifically bind Aβ42 and colocalize into mitochondria in the cellular environment, suggesting the rescue of cell viability might be due to the protection of mitochondrial function otherwise impaired by Aβ42 aggregation. Taken together, our studies indicated that sulfonyl-γ-AApeptides as helical peptidomimetics could direct Aβ into the off-pathway helical secondary structure, thereby preventing the formation of Aβ oligomerization, fibrillation and rescuing Aβ induced cell cytotoxicity.
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Affiliation(s)
- Heng Liu
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Yunpeng Cui
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xue Zhao
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Lulu Wei
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xudong Wang
- Department of Molecular Biosciences, University of South Florida, Tampa, FL33620
| | - Ning Shen
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Timothy Odom
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Xuming Li
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - William Lawless
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | | | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL33620
| | - Wayne Guida
- Department of Chemistry, University of South Florida, Tampa, FL33620
| | - Chuanhai Cao
- Taneja College of Pharmacy, University of South Florida, Tampa, FL33612
| | - Libin Ye
- Department of Molecular Biosciences, University of South Florida, Tampa, FL33620
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL33620
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3
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [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: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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4
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Muschol M, Hoyer W. Amyloid oligomers as on-pathway precursors or off-pathway competitors of fibrils. Front Mol Biosci 2023; 10:1120416. [PMID: 36845541 PMCID: PMC9947291 DOI: 10.3389/fmolb.2023.1120416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Amyloid Diseases involve the growth of disease specific proteins into amyloid fibrils and their deposition in protein plaques. Amyloid fibril formation is typically preceded by oligomeric intermediates. Despite significant efforts, the specific role fibrils or oligomers play in the etiology of any given amyloid disease remains controversial. In neurodegenerative disease, though, amyloid oligomers are widely considered critical contributors to disease symptoms. Aside from oligomers as inevitable on-pathway precursors of fibril formation, there is significant evidence for off-pathway oligomer formation competing with fibril growth. The distinct mechanisms and pathways of oligomer formation directly affect our understanding under which conditions oligomers emerge in vivo, and whether their formation is directly coupled to, or distinct from, amyloid fibril formation. In this review, we will discuss the basic energy landscapes underlying the formation of on-pathway vs. off-pathway oligomers, their relation to the related amyloid aggregation kinetics, and their resulting implications for disease etiology. We will review evidence on how differences in the local environment of amyloid assembly can dramatically shift the relative preponderance of oligomers vs. fibrils. Finally, we will comment on gaps in our knowledge of oligomer assembly, of their structure, and on how to assess their relevance to disease etiology.
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Affiliation(s)
- Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL, United States,*Correspondence: Martin Muschol, ; Wolfgang Hoyer,
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany,Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,*Correspondence: Martin Muschol, ; Wolfgang Hoyer,
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5
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Grelich-Mucha M, Lipok M, Różycka M, Samoć M, Olesiak-Bańska J. One- and Two-Photon Excited Autofluorescence of Lysozyme Amyloids. J Phys Chem Lett 2022; 13:4673-4681. [PMID: 35605187 PMCID: PMC9169060 DOI: 10.1021/acs.jpclett.2c00570] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Autofluorescence properties of amyloid fibrils are of much interest but, to date, the attention has been given mostly to one-photon excited fluorescence (1PEF), while the two-photon excited fluorescence (2PEF) properties of amyloids are much less explored. We investigate 1PEF and 2PEF of hen egg-white lysozyme (HEWL) in the form of monomers and fibrils. HEWL monomers feature some autofluorescence, which is enhanced in the case of fibrils. Moreover, by varying NaCl content, we introduce changes to fibrils morphology and show how the increase of the salt concentration is linked with an increase of 1PEF and 2PEF intensities. Interestingly, we observe 2PEF emission red-shifted in comparison to 1PEF. We confirm the presence of different relaxation pathways upon one- or two-photon excitation by different lifetimes of the fluorescence decays. Finally, we correlate the changes in optical properties of HEWL fibrils and monomers with salt-mediated changes in their morphology and the secondary structure.
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Affiliation(s)
- Manuela Grelich-Mucha
- Advanced
Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Maciej Lipok
- Advanced
Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Mirosława Różycka
- Department
of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Marek Samoć
- Advanced
Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Advanced
Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
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6
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Niyangoda C, Barton J, Bushra N, Karunarathne K, Strauss G, Fakhre F, Koria P, Muschol M. Origin, toxicity and characteristics of two amyloid oligomer polymorphs. RSC Chem Biol 2021; 2:1631-1642. [PMID: 34977578 PMCID: PMC8637835 DOI: 10.1039/d1cb00081k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
There is compelling evidence that small oligomeric aggregates, emerging during the assembly of amyloid fibrils and plaques, are important molecular pathogens in many amyloid diseases. While significant progress has been made in revealing the mechanisms underlying fibril growth, understanding how amyloid oligomers fit into the fibril assembly process, and how they contribute to the pathogenesis of amyloid diseases, has remained elusive. Commonly, amyloid oligomers are considered to be metastable, early-stage precursors to fibril formation that are either on- or off-pathway from fibril growth. In addition, amyloid oligomers have been reported to colocalize with late-stage fibrils and plaques. Whether these early and late-stage oligomer species are identical or distinct, and whether both are relevant to pathogenesis remains unclear. Here we report on the formation of two distinct oligomer species of lysozyme, formed either during the early or late-stages of in vitro fibril growth. We further observe that the pH change from in vitro growth conditions to cell media used for toxicity studies induced distinct mesoscopic precipitates, two of which resemble either diffuse or neuritic plaques seen in Alzheimer's histology. Our biophysical characterization indicates that both oligomer species share morphological and tinctorial features considered characteristic for amyloid oligomers. At the same time, their sizes, morphologies, their immunostaining, detailed tinctorial profiles and, most prominently, their biological activity are clearly distinct from each other. Probing the conditions promoting the formation of these two distinct oligomer species suggests distinct roles of charge interactions, hydrophobicity and monomer flexibility in directing oligomer assembly.
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Affiliation(s)
| | - Jeremy Barton
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
| | - Nabila Bushra
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
| | | | - Graham Strauss
- Dept. of Chemical and Biomedical Engineering, University of South Florida Tampa FL 33620 USA
| | - Fadia Fakhre
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
| | - Piyush Koria
- Dept. of Chemical and Biomedical Engineering, University of South Florida Tampa FL 33620 USA
| | - Martin Muschol
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
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7
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Kummer N, Wu T, De France KJ, Zuber F, Ren Q, Fischer P, Campioni S, Nyström G. Self-Assembly Pathways and Antimicrobial Properties of Lysozyme in Different Aggregation States. Biomacromolecules 2021; 22:4327-4336. [PMID: 34533934 DOI: 10.1021/acs.biomac.1c00870] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Antimicrobial resistance in microorganisms will cause millions of deaths and pose a vast burden on health systems; therefore, alternatives to existing small-molecule antibiotics have to be developed. Lysozyme is an antimicrobial enzyme and has broad-spectrum antimicrobial activity in different aggregated forms. Here, we propose a reductive pathway to obtain colloidally stable amyloid-like worm-shaped lysozyme nanoparticles (worms) from hen egg white lysozyme (HEWL) and compare them to amyloid fibrils made in an acid hydrolysis pathway. The aggregation of HEWL into worms follows strongly pH-dependent kinetics and induces a structural transition from α-helices to β-sheets. Both HEWL worms and amyloid fibrils show broad-spectrum antimicrobial activity against the bacteria Staphylococcus aureus (Gram-positive), Escherichia coli (Gram-negative), and the fungus Candida albicans. The colloidal stability of the worms allows the determination of minimum inhibitory concentrations, which are lower than that for native HEWL in the case of S. aureus. Overall, amyloid fibrils have the strongest antimicrobial effect, likely due to the increased positive charge compared to native HEWL. The structural and functional characterizations of HEWL worms and amyloids investigated herein are critical for understanding the detailed mechanisms of antimicrobial activity and opens up new avenues for the design of broad-spectrum antimicrobial materials for use in various applications.
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Affiliation(s)
- Nico Kummer
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland.,Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Tingting Wu
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland.,State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, 201620 Shanghai, P. R. China
| | - Kevin J De France
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Flavia Zuber
- Laboratory for Biointerfaces, Empa-Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Qun Ren
- Laboratory for Biointerfaces, Empa-Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Peter Fischer
- Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Silvia Campioni
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Gustav Nyström
- Laboratory for Cellulose & Wood Materials, Empa-Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland.,Institute of Food Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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8
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Nakajima K, Toda H, Yamaguchi K, So M, Ikenaka K, Mochizuki H, Goto Y, Ogi H. Half-Time Heat Map Reveals Ultrasonic Effects on Morphology and Kinetics of Amyloidogenic Aggregation Reaction. ACS Chem Neurosci 2021; 12:3456-3466. [PMID: 34467753 DOI: 10.1021/acschemneuro.1c00461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ultrasonication has been recently adopted in amyloid-fibril assays because of its ability to accelerate fibril formation, being promising in the early stage diagnosis of amyloidoses in clinical applications. Although applications of this technique are expanding in the field of protein science, its effects on the aggregation reactions of amyloidogenic proteins are poorly understood. In this study, we comprehensively investigated the morphology and structure of resultant aggregates, kinetics of fibril formation, and seed-detection sensitivity under ultrasonication using β2-microglobulin and compared these characteristics under shaking, which has been traditionally adopted in amyloid-fibril assays. To discuss the ultrasonic effects on the amyloid-fibril formation, we propose the half-time heat map, which describes the phase diagram of the aggregation reaction of amyloidogenic proteins. The experimental results show that ultrasonication greatly promotes fibril formation, especially in dilute monomer solutions, induces short-dispersed fibrils, and is capable of detecting ultra-trace-concentration seeds with a detection limit of 10 fM. Furthermore, we indicate that ultrasonication highly alters the energy landscape of an aggregation reaction due to the effect of ultrasonic cavitation. These insights contribute not only to our understanding of the effects of agitation on amyloidogenic aggregation reactions but also to their effective application in the clinical diagnosis of amyloidoses.
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Affiliation(s)
- Kichitaro Nakajima
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hajime Toda
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masatomo So
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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9
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Xie W, Kim KH, Vince R, More SS. The Amyloid Aggregation Accelerator Diacetyl Prevents Cognitive Decline in Alzheimer's Mouse Models. Chem Res Toxicol 2021; 34:1355-1366. [PMID: 33857375 DOI: 10.1021/acs.chemrestox.1c00089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diacetyl (DA), a food flavorant, is linked with occupational lung disease. Our in vitro experiments described the formation of a covalent adduct by DA with Arg5 of the Aβ1-42 peptide, which resulted in only a transient increase in neurotoxicity in SH-SY5Y cells. However, in vivo implications of these effects on Alzheimer's disease (AD) pathogenesis and the underlying mechanisms remain poorly understood. In the APP/PS1 transgenic AD mouse model, DA treatment did not exacerbate learning and memory deficits in the Morris water maze test. Moreover, DA increased the Aβ1-42 plaque burden and decreased neuronal inflammation in the transgenic AD mice. Additionally, cognitive impairment induced by intracerebroventricular Aβ1-42 was restored by the DA treatment, as assessed by the T-maze test. A corresponding mitigation of neuronal inflammation was also observed in the hippocampus of these nontransgenic mice due to the acceleration of Aβ1-42 aggregation by DA into nontoxic plaques. The data from SDS-PAGE, dot-blot, and TEM in vitro experiments corroborated the acceleration of the Aβ1-42 aggregation observed in vivo in AD animal models and characterized the DA-induced formation of Aβ1-42 fibrils. Such Aβ1-42-DA fibrils were unstable in the presence of detergent and amenable to detection by the thioflavin T reagent, thus underscoring the distinct assembly of these fibrils compared to that of the fibrils of the native Aβ1-42. Taken together, the results of this study present for the first time the in vivo implications of the DA-induced acceleration of Aβ1-42 and may provide a strategy for the rational design of Aβ1-42 aggregation accelerators as AD therapeutics that promote oligomer-free Aβ1-42 fibril formation.
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Affiliation(s)
- Wei Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kwan Hyun Kim
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert Vince
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Swati S More
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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10
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Catalini S, Perinelli DR, Sassi P, Comez L, Palmieri GF, Morresi A, Bonacucina G, Foggi P, Pucciarelli S, Paolantoni M. Amyloid Self-Assembly of Lysozyme in Self-Crowded Conditions: The Formation of a Protein Oligomer Hydrogel. Biomacromolecules 2021; 22:1147-1158. [PMID: 33600168 PMCID: PMC8023603 DOI: 10.1021/acs.biomac.0c01652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A method
is designed to quickly form protein hydrogels, based on
the self-assembly of highly concentrated lysozyme solutions in acidic
conditions. Their properties can be easily modulated by selecting
the curing temperature. Molecular insights on the gelation pathway,
derived by in situ FTIR spectroscopy, are related to calorimetric
and rheological results, providing a consistent picture on structure–property
correlations. In these self-crowded samples, the thermal unfolding
induces the rapid formation of amyloid aggregates, leading to temperature-dependent
quasi-stationary levels of antiparallel cross β-sheet links,
attributed to kinetically trapped oligomers. Upon subsequent cooling,
thermoreversible hydrogels develop by the formation of interoligomer
contacts. Through heating/cooling cycles, the starting solutions can
be largely recovered back, due to oligomer-to-monomer dissociation
and refolding. Overall, transparent protein hydrogels can be easily
formed in self-crowding conditions and their properties explained,
considering the formation of interconnected amyloid oligomers. This
type of biomaterial might be relevant in different fields, along with
analogous systems of a fibrillar nature more commonly considered.
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Affiliation(s)
- Sara Catalini
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, 50019 Sesto Fiorentino, Italy
| | | | - Paola Sassi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, University of Perugia, 060123 Perugia, Italy
| | | | - Assunta Morresi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | - Paolo Foggi
- European Laboratory for Non-Linear Spectroscopy (LENS), University of Florence, 50019 Sesto Fiorentino, Italy.,Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy.,National Metrological Research Institute (INRIM), Strada delle Cacce 91, 10135 Torino, Italy
| | - Stefania Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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11
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Nakajima K, Yamazaki T, Kimura Y, So M, Goto Y, Ogi H. Time-Resolved Observation of Evolution of Amyloid-β Oligomer with Temporary Salt Crystals. J Phys Chem Lett 2020; 11:6176-6184. [PMID: 32687370 DOI: 10.1021/acs.jpclett.0c01487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aggregation behavior of amyloid-β (Aβ) peptides remains unclarified despite the fact that it is closely related to the pathogenic mechanism of Alzheimer's disease. Aβ peptides form diverse oligomers with various diameters before nucleation, making clarification of the mechanism involved a complex problem with conventional macroscopic analysis methods. Time-resolved single-molecule level analysis in bulk solution is thus required to fully understand their early stage aggregation behavior. Here, we perform time-resolved observation of the aggregation dynamics of Aβ oligomers in bulk solution using liquid-state transmission electron microscopy. Our observations reveal previously unknown behaviors. The most important discovery is that a salt crystal can precipitate even with a concentration much lower than its solubility, and it then dissolves in a short time, during which the aggregation reaction of Aβ peptides is significantly accelerated. These findings will provide new insights in the evolution of the Aβ oligomer.
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Affiliation(s)
- Kichitaro Nakajima
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoya Yamazaki
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Yuki Kimura
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-8638, Japan
| | - Masatomo So
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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12
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Barton J, Arias DS, Niyangoda C, Borjas G, Le N, Mohamed S, Muschol M. Kinetic Transition in Amyloid Assembly as a Screening Assay for Oligomer-Selective Dyes. Biomolecules 2019; 9:biom9100539. [PMID: 31569739 PMCID: PMC6843685 DOI: 10.3390/biom9100539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 02/06/2023] Open
Abstract
Assembly of amyloid fibrils and small globular oligomers is associated with a significant number of human disorders that include Alzheimer’s disease, senile systemic amyloidosis, and type II diabetes. Recent findings implicate small amyloid oligomers as the dominant aggregate species mediating the toxic effects in these disorders. However, validation of this hypothesis has been hampered by the dearth of experimental techniques to detect, quantify, and discriminate oligomeric intermediates from late-stage fibrils, in vitro and in vivo. We have shown that the onset of significant oligomer formation is associated with a transition in thioflavin T kinetics from sigmoidal to biphasic kinetics. Here we showed that this transition can be exploited for screening fluorophores for preferential responses to oligomer over fibril formation. This assay identified crystal violet as a strongly selective oligomer-indicator dye for lysozyme. Simultaneous recordings of amyloid kinetics with thioflavin T and crystal violet enabled us to separate the combined signals into their underlying oligomeric and fibrillar components. We provided further evidence that this screening assay could be extended to amyloid-β peptides under physiological conditions. Identification of oligomer-selective dyes not only holds the promise of biomedical applications but provides new approaches for unraveling the mechanisms underlying oligomer versus fibril formation in amyloid assembly.
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Affiliation(s)
- Jeremy Barton
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - D Sebastian Arias
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Chamani Niyangoda
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Gustavo Borjas
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Nathan Le
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Saefallah Mohamed
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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13
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Konar M, Mathew A, Dasgupta S. Effect of Silica Nanoparticles on the Amyloid Fibrillation of Lysozyme. ACS OMEGA 2019; 4:1015-1026. [PMID: 31459377 PMCID: PMC6648903 DOI: 10.1021/acsomega.8b03169] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/28/2018] [Indexed: 05/18/2023]
Abstract
Protein fibrils are regarded as undesired products as these are associated with numerous neuro- and non-neurodegenerative disorders. Increasing evidence suggests that the mechanism of fibrillation involves the formation of various oligomeric intermediates, which are known to be more toxic than mature fibrils. Here, we report the impact of synthesized silica nanoparticles (SiNPs) of diameters ∼52 nm on the aggregation behavior of hen egg white lysozyme (HEWL) under heat and acidic conditions. Congo red as well as ThT binding assays and AFM imaging studies indicate that SiNPs trigger the amyloid formation of HEWL in a dose-dependent manner. ThT kinetic studies and FTIR studies suggest that the fibrillation kinetics does not involve the formation of toxic oligomeric intermediates at higher concentrations of SiNPs. By measuring fluorescence lifetime values of the bound ThT, SiNP-induced fibrillation of HEWL can easily be realized. CD spectroscopic studies indicate that native HEWL becomes unfolded upon incubation under the experimental conditions and is rapidly converted into the β-sheet-rich fibrillar aggregates in the presence of SiNPs with increasing concentrations. It has been further revealed that fibrillar aggregates formed at higher concentrations of SiNPs preferably adopt an antiparallel β-sheet configuration. The enhanced fibrillation in the presence of SiNPs is likely because of preferential adsorption of the non-amyloidogenic regions of HEWL, resulting in the exposure of the aggregation-prone regions of HEWL toward the solvent. The study will provide deeper insights into the evolution of oligomer-free fibrillation that can be useful to demonstrate the underlying mechanism of amyloid fibrillation.
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14
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Hasecke F, Miti T, Perez C, Barton J, Schölzel D, Gremer L, Grüning CSR, Matthews G, Meisl G, Knowles TPJ, Willbold D, Neudecker P, Heise H, Ullah G, Hoyer W, Muschol M. Origin of metastable oligomers and their effects on amyloid fibril self-assembly. Chem Sci 2018; 9:5937-5948. [PMID: 30079208 PMCID: PMC6050532 DOI: 10.1039/c8sc01479e] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023] Open
Abstract
Assembly of rigid amyloid fibrils with their characteristic cross-β sheet structure is a molecular signature of numerous neurodegenerative and non-neuropathic disorders. Frequently large populations of small globular amyloid oligomers (gOs) and curvilinear fibrils (CFs) precede the formation of late-stage rigid fibrils (RFs), and have been implicated in amyloid toxicity. Yet our understanding of the origin of these metastable oligomers, their role as on-pathway precursors or off-pathway competitors, and their effects on the self-assembly of amyloid fibrils remains incomplete. Using two unrelated amyloid proteins, amyloid-β and lysozyme, we find that gO/CF formation, analogous to micelle formation by surfactants, is delineated by a "critical oligomer concentration" (COC). Below this COC, fibril assembly replicates the sigmoidal kinetics of nucleated polymerization. Upon crossing the COC, assembly kinetics becomes biphasic with gO/CF formation responsible for the lag-free initial phase, followed by a second upswing dominated by RF nucleation and growth. RF lag periods below the COC, as expected, decrease as a power law in monomer concentration. Surprisingly, the build-up of gO/CFs above the COC causes a progressive increase in RF lag periods. Our results suggest that metastable gO/CFs are off-pathway from RF formation, confined by a condition-dependent COC that is distinct from RF solubility, underlie a transition from sigmoidal to biphasic assembly kinetics and, most importantly, not only compete with RFs for the shared monomeric growth substrate but actively inhibit their nucleation and growth.
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Affiliation(s)
- Filip Hasecke
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
| | - Tatiana Miti
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Carlos Perez
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Jeremy Barton
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Daniel Schölzel
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Lothar Gremer
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Clara S R Grüning
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
| | - Garrett Matthews
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Dieter Willbold
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Philipp Neudecker
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Henrike Heise
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Ghanim Ullah
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Martin Muschol
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
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15
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Niyangoda C, Miti T, Breydo L, Uversky V, Muschol M. Carbonyl-based blue autofluorescence of proteins and amino acids. PLoS One 2017; 12:e0176983. [PMID: 28542206 PMCID: PMC5444599 DOI: 10.1371/journal.pone.0176983] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/20/2017] [Indexed: 11/29/2022] Open
Abstract
Intrinsic protein fluorescence is inextricably linked to the near-UV autofluorescence of aromatic amino acids. Here we show that a novel deep-blue autofluorescence (dbAF), previously thought to emerge as a result of protein aggregation, is present at the level of monomeric proteins and even poly- and single amino acids. Just as its aggregation-related counterpart, this autofluorescence does not depend on aromatic residues, can be excited at the long wavelength edge of the UV and emits in the deep blue. Differences in dbAF excitation and emission peaks and intensities from proteins and single amino acids upon changes in solution conditions suggest dbAF’s sensitivity to both the chemical identity and solution environment of amino acids. Autofluorescence comparable to dbAF is emitted by carbonyl-containing organic solvents, but not those lacking the carbonyl group. This implicates the carbonyl double bonds as the likely source for the autofluorescence in all these compounds. Using beta-lactoglobulin and proline, we have measured the molar extinction coefficients and quantum yields for dbAF in the monomeric state. To establish its potential utility in monitoring protein biophysics, we show that dbAF emission undergoes a red-shift comparable in magnitude to tryptophan upon thermal denaturation of lysozyme, and that it is sensitive to quenching by acrylamide. Carbonyl dbAF therefore provides a previously neglected intrinsic optical probe for investigating the structure and dynamics of amino acids, proteins and, by extension, DNA and RNA.
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Affiliation(s)
- Chamani Niyangoda
- Department of Physics, University of South Florida, Tampa, Florida, United States of America
| | - Tatiana Miti
- Department of Physics, University of South Florida, Tampa, Florida, United States of America
| | - Leonid Breydo
- Department of Molecular Medicine, USF Health, Tampa, Florida, United States of America
| | - Vladimir Uversky
- Department of Molecular Medicine, USF Health, Tampa, Florida, United States of America
| | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, Florida, United States of America
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16
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Chaari A, Fahy C, Chevillot-Biraud A, Rholam M. Insights into Kinetics of Agitation-Induced Aggregation of Hen Lysozyme under Heat and Acidic Conditions from Various Spectroscopic Methods. PLoS One 2015; 10:e0142095. [PMID: 26571264 PMCID: PMC4646502 DOI: 10.1371/journal.pone.0142095] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 01/28/2023] Open
Abstract
Protein misfolding and amyloid formation are an underlying pathological hallmark in a number of prevalent diseases of protein aggregation ranging from Alzheimer’s and Parkinson’s diseases to systemic lysozyme amyloidosis. In this context, we have used complementary spectroscopic methods to undertake a systematic study of the self-assembly of hen egg-white lysozyme under agitation during a prolonged heating in acidic pH. The kinetics of lysozyme aggregation, monitored by Thioflavin T fluorescence, dynamic light scattering and the quenching of tryptophan fluorescence by acrylamide, is described by a sigmoid curve typical of a nucleation-dependent polymerization process. Nevertheless, we observe significant differences between the values deduced for the kinetic parameters (lag time and aggregation rate). The fibrillation process of lysozyme, as assessed by the attenuated total reflection-Fourier transform infrared spectroscopy, is accompanied by an increase in the β-sheet conformation at the expense of the α-helical conformation but the time-dependent variation of the content of these secondary structures does not evolve as a gradual transition. Moreover, the tryptophan fluorescence-monitored kinetics of lysozyme aggregation is described by three phases in which the temporal decrease of the tryptophan fluorescence quantum yield is of quasilinear nature. Finally, the generated lysozyme fibrils exhibit a typical amyloid morphology with various lengths (observed by atomic force microscopy) and contain exclusively the full-length protein (analyzed by highly performance liquid chromatography). Compared to the data obtained by other groups for the formation of lysozyme fibrils in acidic pH without agitation, this work provides new insights into the structural changes (local, secondary, oligomeric/fibrillar structures) undergone by the lysozyme during the agitation-induced formation of fibrils.
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Affiliation(s)
- Ali Chaari
- ITODYS, UMR CNRS 7086, Univ. Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
- Laboratoire de Génétique et Biologie Cellulaire, Université de Versailles Saint-Quentin-en-Yvelines, 78035, Versailles, France
| | - Christine Fahy
- ITODYS, UMR CNRS 7086, Univ. Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | | | - Mohamed Rholam
- ITODYS, UMR CNRS 7086, Univ. Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
- * E-mail:
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17
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Giugliarelli A, Tarpani L, Latterini L, Morresi A, Paolantoni M, Sassi P. Spectroscopic and Microscopic Studies of Aggregation and Fibrillation of Lysozyme in Water/Ethanol Solutions. J Phys Chem B 2015; 119:13009-17. [DOI: 10.1021/acs.jpcb.5b07487] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Alessandra Giugliarelli
- Dipartimento di Chimica, Biologia e Biotecnologie and ‡Dipartimento di
Chimica, Biologia
e Biotecnologie and Centro di Eccellenza Materiali Innovativi Nanostrutturati
CEMIN, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Luigi Tarpani
- Dipartimento di Chimica, Biologia e Biotecnologie and ‡Dipartimento di
Chimica, Biologia
e Biotecnologie and Centro di Eccellenza Materiali Innovativi Nanostrutturati
CEMIN, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie and ‡Dipartimento di
Chimica, Biologia
e Biotecnologie and Centro di Eccellenza Materiali Innovativi Nanostrutturati
CEMIN, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento di Chimica, Biologia e Biotecnologie and ‡Dipartimento di
Chimica, Biologia
e Biotecnologie and Centro di Eccellenza Materiali Innovativi Nanostrutturati
CEMIN, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Biologia e Biotecnologie and ‡Dipartimento di
Chimica, Biologia
e Biotecnologie and Centro di Eccellenza Materiali Innovativi Nanostrutturati
CEMIN, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Biologia e Biotecnologie and ‡Dipartimento di
Chimica, Biologia
e Biotecnologie and Centro di Eccellenza Materiali Innovativi Nanostrutturati
CEMIN, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
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18
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Stehli D, Mulaj M, Miti T, Traina J, Foley J, Muschol M. Collapsed state of polyglutamic acid results in amyloid spherulite formation. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1056905. [PMID: 28232889 DOI: 10.1080/21690707.2015.1056905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
Self-assembly of proteins and peptides into amyloid fibrils involves multiple distinct intermediates and late-stage fibrillar polymorphs. Understanding the conditions and mechanisms that promote the formation of one type of intermediate and polymorph over the other represents a fundamental challenge. Answers to this question are also of immediate biomedical relevance since different amyloid aggregate species have been shown to have distinct pathogenic potencies. One amyloid polymorph that has received comparatively little attention are amyloid spherulites. Here we report that self-assembly of the intrinsically disordered polymer poly(L-glutamic) acid (PLE) can generate amyloid spherulites. We characterize spherulite growth kinetics, as well as the morphological, optical and tinctorial features of this amyloid polymorph previously unreported for PLE. We find that PLE spherulites share both tinctorial and structural characteristics with their amyloid fibril counterparts. Differences in PLE's molecular weight, polydispersity or chemistry could not explain the selective propensity toward either fibril or spherulite formation. Instead, we provide evidence that PLE polymers can exist in either a collapsed globule or an extended random coil conformation. The collapsed globule consistently produces spherulites while the extended coil assembles into disordered fibril bundles. This results suggests that these 2 PLE conformers directly affect the morphology of the resulting macroscopic amyloid assembly.
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Affiliation(s)
- Daniel Stehli
- Department of Physics; University of South Florida ; Tampa, FL USA
| | - Mentor Mulaj
- Department of Physics; University of South Florida ; Tampa, FL USA
| | - Tatiana Miti
- Department of Physics; University of South Florida ; Tampa, FL USA
| | - Joshua Traina
- Department of Physics; University of South Florida ; Tampa, FL USA
| | - Joseph Foley
- Department of Physics; University of South Florida ; Tampa, FL USA
| | - Martin Muschol
- Department of Physics; University of South Florida ; Tampa, FL USA
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19
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Miti T, Mulaj M, Schmit JD, Muschol M. Stable, metastable, and kinetically trapped amyloid aggregate phases. Biomacromolecules 2014; 16:326-35. [PMID: 25469942 PMCID: PMC4294590 DOI: 10.1021/bm501521r] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Self-assembly of proteins into amyloid fibrils plays a key role in a multitude of human disorders that range from Alzheimer's disease to type II diabetes. Compact oligomeric species, observed early during amyloid formation, are reported as the molecular entities responsible for the toxic effects of amyloid self-assembly. However, the relation between early-stage oligomeric aggregates and late-stage rigid fibrils, which are the hallmark structure of amyloid plaques, has remained unclear. We show that these different structures occupy well-defined regions in a peculiar phase diagram. Lysozyme amyloid oligomers and their curvilinear fibrils only form after they cross a salt and protein concentration-dependent threshold. We also determine a boundary for the onset of amyloid oligomer precipitation. The oligomeric aggregates are structurally distinct from rigid fibrils and are metastable against nucleation and growth of rigid fibrils. These experimentally determined boundaries match well with colloidal model predictions that account for salt-modulated charge repulsion. The model also incorporates the metastable and kinetic character of oligomer phases. Similarities and differences of amyloid oligomer assembly to metastable liquid-liquid phase separation of proteins and to surfactant aggregation are discussed.
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Affiliation(s)
- Tatiana Miti
- Department of Physics, University of South Florida , Tampa, Florida 33620, United States
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20
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Mulaj M, Foley J, Muschol M. Amyloid oligomers and protofibrils, but not filaments, self-replicate from native lysozyme. J Am Chem Soc 2014; 136:8947-56. [PMID: 24884889 PMCID: PMC4227717 DOI: 10.1021/ja502529m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Self-assembly
of amyloid fibrils is the molecular mechanism best
known for its connection with debilitating human disorders such as
Alzheimer’s disease but is also associated with various functional
cellular responses. There is increasing evidence that amyloid formation
proceeds along two distinct assembly pathways involving either globular
oligomers and protofibrils or rigid monomeric filaments. Oligomers,
in particular, have been implicated as the dominant molecular species
responsible for pathogenesis. Yet the molecular mechanisms regulating
their self-assembly have remained elusive. Here we show that oligomers/protofibrils
and monomeric filaments, formed along distinct assembly pathways,
display critical differences in their ability to template amyloid
growth at physiological vs denaturing temperatures. At physiological
temperatures, amyloid filaments remained stable but could not seed
growth of native monomers. In contrast, oligomers and protofibrils
not only remained intact but were capable of self-replication using
native monomers as the substrate. Kinetic data further suggested that
this prion-like growth mode of oligomers/protofibrils involved two
distinct activities operating orthogonal from each other: autocatalytic
self-replication of oligomers from native monomers and nucleated polymerization
of oligomers into protofibrils. The environmental changes to stability
and templating competence of these different amyloid species in different
environments are likely to be important for understanding the molecular
mechanisms underlying both pathogenic and functional amyloid self-assembly.
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Affiliation(s)
- Mentor Mulaj
- Department of Physics, University of South Florida , Tampa, Florida 33620, United States
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21
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Conformational targeting of intracellular Aβ oligomers demonstrates their pathological oligomerization inside the endoplasmic reticulum. Nat Commun 2014; 5:3867. [PMID: 24861166 PMCID: PMC4050278 DOI: 10.1038/ncomms4867] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 04/10/2014] [Indexed: 01/18/2023] Open
Abstract
Aβ oligomers (AβOs) are crucially involved in Alzheimer’s Disease (AD). However, the lack of selective approaches for targeting these polymorphic Aβ assemblies represents a major hurdle in understanding their biosynthesis, traffic and actions in living cells. Here, we established a subcellularly localized conformational-selective interference (CSI) approach, based on the expression of a recombinant antibody fragment against AβOs in the endoplasmic reticulum (ER). By CSI, we can control extra- and intracellular pools of AβOs produced in an AD-relevant cell model, without interfering with the maturation and processing of the Aβ precursor protein. The anti-AβOs intrabody selectively intercepts critical AβO conformers in the ER, modulating their assembly and controlling their actions in pathways of cellular homeostasis and synaptic signalling. Our results demonstrate that intracellular Aβ undergoes pathological oligomerization through critical conformations formed inside the ER. This establishes intracellular AβOs as key targets for AD treatment and presents CSI as a potential targeting strategy. Intracellular Aß oligomers have been linked to Alzheimer’s disease but details about their biosynthesis and function have been hard to obtain due to the lack of selective approaches for targeting them. Here, Meli et al. develop a strategy using recombinant antibodies to target Aß oligomers in the endoplasmic reticulum of cells, and perform mechanistic studies in cellular models of the disease.
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22
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Hill SE, Donegan RK, Lieberman RL. The glaucoma-associated olfactomedin domain of myocilin forms polymorphic fibrils that are constrained by partial unfolding and peptide sequence. J Mol Biol 2013; 426:921-35. [PMID: 24333014 DOI: 10.1016/j.jmb.2013.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/06/2013] [Accepted: 12/02/2013] [Indexed: 12/26/2022]
Abstract
The glaucoma-associated olfactomedin domain of myocilin (myoc-OLF) is a recent addition to the growing list of disease-associated amyloidogenic proteins. Inherited, disease-causing myocilin variants aggregate intracellularly instead of being secreted to the trabecular meshwork, which is a scenario toxic to trabecular meshwork cells and leads to early onset of ocular hypertension, the major risk factor for glaucoma. Here we systematically structurally and biophysically dissected myoc-OLF to better understand its amyloidogenesis. Under mildly destabilizing conditions, wild-type myoc-OLF adopts non-native structures that readily fibrillize when incubated at a temperature just below the transition for tertiary unfolding. With buffers at physiological pH, two main endpoint fibril morphologies are observed: (a) straight fibrils common to many amyloids and (b) unique micron-length, ~300 nm or larger diameter, species that lasso oligomers, which also exhibit classical spectroscopic amyloid signatures. Three disease-causing variants investigated herein exhibit non-native tertiary structures under physiological conditions, leading to a variety of growth rates and a fibril morphologies. In particular, the well-documented D380A variant, which lacks calcium, forms large circular fibrils. Two amyloid-forming peptide stretches have been identified, one for each of the main fibril morphologies observed. Our study places myoc-OLF within the larger landscape of the amylome and provides insight into the diversity of myoc-OLF aggregation that plays a role in glaucoma pathogenesis.
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Affiliation(s)
- Shannon E Hill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive Northwest, Atlanta, GA 30332-0400, USA
| | - Rebecca K Donegan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive Northwest, Atlanta, GA 30332-0400, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive Northwest, Atlanta, GA 30332-0400, USA.
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23
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Gruebele M, Thirumalai D. Perspective: Reaches of chemical physics in biology. J Chem Phys 2013; 139:121701. [PMID: 24089712 PMCID: PMC5942441 DOI: 10.1063/1.4820139] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/20/2013] [Indexed: 01/09/2023] Open
Abstract
Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.
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Affiliation(s)
- Martin Gruebele
- Departments of Chemistry and Physics, and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, USA
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