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Pagano K, De Rosa L, Tomaselli S, Molinari H, D'Andrea LD, Ragona L. Characterizing the Oligomers Distribution along the Aggregation Pathway of Amyloid Aβ1-40 by NMR. Chemistry 2024; 30:e202400594. [PMID: 38712990 DOI: 10.1002/chem.202400594] [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: 02/13/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
This study delves into the early aggregation process of the Aβ1-40 amyloid peptide, elucidating the associated oligomers distribution. Motivated by the acknowledged role of small oligomers in the neurotoxic damage linked to Alzheimer's disease, we present an experimental protocol for preparing 26-O-acyl isoAβ1-40, a modified Aβ1-40 peptide facilitating rapid isomerization to the native amide form at neutral pH. This ensures seed-free solutions, minimizing experimental variability. Additionally, we demonstrate the efficacy of coupling NMR diffusion ordered spectroscopy (DOSY) with the Inverse Laplace Transform (ILT) reconstruction method, for effective characterization of early aggregation processes. This innovative approach efficiently maps oligomers distributions across a wide spectrum of initial peptide concentrations offering unique insights into the evolution of oligomers relative populations. As a proof of concept, we demonstrate the efficacy of our approach assessing the impact of Epigallocathechin gallate, a known remodeling agent of amyloid fibrils, on the oligomeric distributions of aggregated Aβ1-40. The DOSY-ILT proposed approach stands as a robust and discriminating asset, providing a powerful strategy for rapidly gaining insight into potential inhibitors' impact on the aggregation process.
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Affiliation(s)
- Katiuscia Pagano
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini CNR, Via Pietro Castellino 111, Napoli, Italy
| | - Simona Tomaselli
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Henriette Molinari
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
| | - Luca Domenico D'Andrea
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, Via Mario Bianco, 9, Milano, Italy
| | - Laura Ragona
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta" CNR, via Alfonso Corti, 12, Milano, Italy
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2
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Ruttenberg SM, Nowick JS. A turn for the worse: Aβ β-hairpins in Alzheimer's disease. Bioorg Med Chem 2024; 105:117715. [PMID: 38615460 DOI: 10.1016/j.bmc.2024.117715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
Amyloid-β (Aβ) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aβ peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aβ oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aβ oligomers, many of which consist of molecules of Aβ in β-hairpin conformations. β-Hairpins are intramolecular antiparallel β-sheets composed of two β-strands connected by a loop or turn. Three decades of research suggests that Aβ peptides form several different β-hairpin conformations, some of which are building blocks of toxic Aβ oligomers. The insights from these studies are currently being used to design anti-Aβ antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aβ may be more successful at treating AD than antibodies designed to target linear epitopes of Aβ or fibrillar Aβ. Aβ β-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aβ. This review summarizes the research on β-hairpins in Aβ peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.
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Affiliation(s)
- Sarah M Ruttenberg
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States.
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3
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Maity B, Kameyama S, Tian J, Pham TT, Abe S, Chatani E, Murata K, Ueno T. Fusion of amyloid beta with ferritin yields an isolated oligomeric beta-sheet-rich aggregate inside the ferritin cage. Biomater Sci 2024; 12:2408-2417. [PMID: 38511491 DOI: 10.1039/d4bm00173g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Alzheimer's disease is a severe brain condition caused by the formation of amyloid plaques composed of amyloid beta (Aβ) peptides. These peptides form oligomers, protofibrils, and fibrils before deposition into amyloid plaques. Among these intermediates, Aβ oligomers (AβOs) were found to be the most toxic and therefore an appealing target for drug development and understanding their role in the disease. However, precise isolation and characterization of AβOs have proven challenging because AβOs tend to aggregate and form heterogeneous mixtures in solution. As a solution, we genetically fused the Aβ peptide with a ferritin monomer. Such fusion allowed the encapsulation of precisely 24 Aβ peptides inside the 24-mer ferritin cage. Using high-speed atomic force microscopy (HS-AFM), we disassembled ferritin and directly visualized the Aβ core enclosed within the cage. The thioflavin-T assay (ThT) and attenuated total reflection infrared spectroscopy (ATR-IR) revealed the presence of a β-sheet structure in the encapsulated oligomeric aggregate. Gallic acid, an amyloid inhibitor, can inhibit the fluorescence of ThT bound AβOs. Our approach represents a significant advancement in the isolation and characterization of β-sheet rich AβOs and is expected to be useful for future studies of other disordered peptides such as α-synuclein and tau.
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Affiliation(s)
- Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Shiori Kameyama
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Jiaxin Tian
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Thuc Toan Pham
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, 444-8585, Japan
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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4
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Saha J, Ford BJ, Wang X, Boyd S, Morgan SE, Rangachari V. Sugar distributions on gangliosides guide the formation and stability of amyloid-β oligomers. Biophys Chem 2023; 300:107073. [PMID: 37413816 PMCID: PMC10529042 DOI: 10.1016/j.bpc.2023.107073] [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: 03/24/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Aggregation of Aβ peptides is a key contributor to the etiology of Alzheimer's disease. Being intrinsically disordered, monomeric Aβ is susceptible to conformational excursions, especially in the presence of important interacting partners such as membrane lipids, to adopt specific aggregation pathways. Furthermore, components such as gangliosides in membranes and lipid rafts are known to play important roles in the adoption of pathways and the generation of discrete neurotoxic oligomers. Yet, what roles do carbohydrates on gangliosides play in this process remains unknown. Here, using GM1, GM3, and GD3 ganglioside micelles as models, we show that the sugar distributions and cationic amino acids within Aβ N-terminal region modulate oligomerization of Aβ temporally, and dictate the stability and maturation of oligomers. These results demonstrate the selectivity of sugar distributions on the membrane surface toward oligomerization of Aβ and thus implicate cell-selective enrichment of oligomers.
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Affiliation(s)
- Jhinuk Saha
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, 118, College Dr Hattiesburg, MS 39402, USA
| | - Brea J Ford
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, 118, College Dr Hattiesburg, MS 39402, USA
| | | | - Sydney Boyd
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, 118, College Dr Hattiesburg, MS 39402, USA
| | | | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences, 118, College Dr Hattiesburg, MS 39402, USA; Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA.
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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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6
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Saha J, Ford BJ, Boyd S, Rangachari V. Sugar distributions on gangliosides guide the formation and stability of amyloid-β oligomers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540003. [PMID: 37214891 PMCID: PMC10197704 DOI: 10.1101/2023.05.09.540003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aggregation of Aβ peptides has been known as a key contributor to the etiology of Alzheimer's disease. Being intrinsically disordered, the monomeric Aβ is susceptible to conformational excursions, especially in the presence of key interacting partners such as membrane lipids, to adopt specific aggregation pathways. Furthermore, key components such as gangliosides in membranes and lipid rafts are known to play important roles in the adoption of pathways and the generation of discrete neurotoxic oligomers. Yet, what roles the carbohydrates on gangliosides play in this process remains unknown. Here, using GM1, GM3, and GD3 ganglioside micelles as models, we show that the sugar distributions and cationic amino acids within Aβ N-terminal region modulate oligomerization of Aβ temporally, and dictate the stability and maturation of oligomers.
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7
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Im D, Kim S, Yoon G, Hyun DG, Eom YG, Lee YE, Sohn CH, Choi JM, Kim HI. Decoding the Roles of Amyloid-β (1-42)'s Key Oligomerization Domains toward Designing Epitope-Specific Aggregation Inhibitors. JACS AU 2023; 3:1065-1075. [PMID: 37124297 PMCID: PMC10131210 DOI: 10.1021/jacsau.2c00668] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 05/03/2023]
Abstract
Fibrillar amyloid aggregates are the pathological hallmarks of multiple neurodegenerative diseases. The amyloid-β (1-42) protein, in particular, is a major component of senile plaques in the brains of patients with Alzheimer's disease and a primary target for disease treatment. Determining the essential domains of amyloid-β (1-42) that facilitate its oligomerization is critical for the development of aggregation inhibitors as potential therapeutic agents. In this study, we identified three key hydrophobic sites (17LVF19, 32IGL34, and 41IA42) on amyloid-β (1-42) and investigated their involvement in the self-assembly process of the protein. Based on these findings, we designed candidate inhibitor peptides of amyloid-β (1-42) aggregation. Using the designed peptides, we characterized the roles of the three hydrophobic regions during amyloid-β (1-42) fibrillar aggregation and monitored the consequent effects on its aggregation property and structural conversion. Furthermore, we used an amyloid-β (1-42) double point mutant (I41N/A42N) to examine the interactions between the two C-terminal end residues with the two hydrophobic regions and their roles in amyloid self-assembly. Our results indicate that interchain interactions in the central hydrophobic region (17LVF19) of amyloid-β (1-42) are important for fibrillar aggregation, and its interaction with other domains is associated with the accessibility of the central hydrophobic region for initiating the oligomerization process. Our study provides mechanistic insights into the self-assembly of amyloid-β (1-42) and highlights key structural domains that facilitate this process. Our results can be further applied toward improving the rational design of candidate amyloid-β (1-42) aggregation inhibitors.
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Affiliation(s)
- Dongjoon Im
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Soohyeong Kim
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Gyusub Yoon
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Da Gyeong Hyun
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
| | - Yu-Gon Eom
- Department
of Chemistry, Pusan National University, Busan 46241, Republic of Korea
| | - Ye Eun Lee
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Chang Ho Sohn
- Center
for Nanomedicine, Institute for Basic Science
(IBS), Seoul 03722, Republic of Korea
- Graduate
Program in Nanobiomedical Engineering, Advanced Science Institute, Yonsei University, Seoul 03722, Republic of Korea
| | - Jeong-Mo Choi
- Department
of Chemistry, Pusan National University, Busan 46241, Republic of Korea
- Chemistry
Institute for Functional Materials, Pusan
National University, Busan 46241, Republic
of Korea
| | - Hugh I. Kim
- Department
of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center
for Proteogenome Research, Korea University, Seoul 02841, Republic of Korea
- Single
Cell Analysis Laboratory, Korea University, Seoul 02841, Republic of Korea
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8
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Ghosh S, Ali R, Verma S. Aβ-oligomers: A potential therapeutic target for Alzheimer's disease. Int J Biol Macromol 2023; 239:124231. [PMID: 36996958 DOI: 10.1016/j.ijbiomac.2023.124231] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
The cascade of amyloid formation relates to multiple complex events at the molecular level. Previous research has established amyloid plaque deposition as the leading cause of Alzheimer's disease (AD) pathogenesis, detected mainly in aged population. The primary components of the plaques are two alloforms of amyloid-beta (Aβ), Aβ1-42 and Aβ1-40 peptides. Recent studies have provided considerable evidence contrary to the previous claim indicating that amyloid-beta oligomers (AβOs) as the main culprit responsible for AD-associated neurotoxicity and pathogenesis. In this review, we have discussed the primary features of AβOs, such as assembly formation, the kinetics of oligomer formation, interactions with various membranes/membrane receptors, the origin of toxicity, and oligomer-specific detection methods. Recently, the discovery of rationally designed antibodies has opened a gateway for using synthesized peptides as a grafting component in the complementarity determining region (CDR) of antibodies. Thus, the Aβ sequence motif or the complementary peptide sequence in the opposite strand of the β-sheet (extracted from the Protein Data Bank: PDB) helps design oligomer-specific inhibitors. The microscopic event responsible for oligomer formation can be targeted, and thus prevention of the overall macroscopic behaviour of the aggregation or the associated toxicity can be achieved. We have carefully reviewed the oligomer formation kinetics and associated parameters. Besides, we have depicted a thorough understanding of how the synthesized peptide inhibitors can impede the early aggregates (oligomers), mature fibrils, monomers, or a mixture of the species. The oligomer-specific inhibitors (peptides or peptide fragments) lack in-depth chemical kinetics and optimization control-based screening. In the present review, we have proposed a hypothesis for effectively screening oligomer-specific inhibitors using the chemical kinetics (determining the kinetic parameters) and optimization control strategy (cost-dependent analysis). Further, it may be possible to implement the structure-kinetic-activity-relationship (SKAR) strategy instead of structure-activity-relationship (SAR) to improve the inhibitor's activity. The controlled optimization of the kinetic parameters and dose usage will be beneficial for narrowing the search window for the inhibitors.
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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: 8] [Impact Index Per Article: 8.0] [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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Morel B, Conejero-Lara F. Preparation and Investigation of Crucial Oligomers in the Early Stages of Aβ40 and Aβ42 Aggregation. Methods Mol Biol 2023; 2551:15-28. [PMID: 36310193 DOI: 10.1007/978-1-0716-2597-2_2] [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] [Indexed: 06/16/2023]
Abstract
Amyloid aggregation is a hallmark in many neuropathologies and other diseases of tremendous impact. It is increasingly evident that neuronal death associated with Alzheimer's disease (AD) is mainly produced by oligomers of the amyloid-β (Aβ) peptide. Yet little is known about the detailed structural and biophysical mechanisms of their formation. This lack of complete understanding comes from the labile nature and handling complexity of the oligomers. Consequently, providing reproducible and robust protocols for oligomer preparation is of particular importance.In this study, we describe detailed methods for the preparation and isolation of micellar oligomers of Aβ that evolve towards larger and more stable oligomers enriched in beta-sheet structure and able to acquire a higher capacity to fibrillate. We also describe briefly some biophysical experiments allowing oligomer characterization.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, Granada, Spain.
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, Granada, Spain.
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11
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Pillai M, Jha SK. Multistep molecular mechanism of amyloid-like aggregation of nucleic acid-binding domain of TDP-43. Proteins 2022; 91:649-664. [PMID: 36530161 DOI: 10.1002/prot.26455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
TDP-43 protein is associated with many neurodegenerative diseases and has been shown to adopt various oligomeric and fibrillar states. However, a detailed kinetic understanding of the structural transformation of the native form of the protein to the fibrillar state is missing. In this study, we delineate the temporal sequence of structural events during the amyloid-like assembly of the functional nucleic acid-binding domain of TDP-43. We kinetically mapped the aggregation process using multiple probes such as tryptophan and thioflavin T (ThT) fluorescence, circular dichroism (CD), and dynamic light scattering (DLS) targeting different structural events. Our data reveal that aggregation occurs in four distinct steps-very fast, fast, slow, and very slow. The "very fast" change results in partially unfolded forms that undergo conformational conversion, oligomerization and bind to ThT in the "fast step" to form higher order intermediates (HOI). The temporal sequence of the formation of ThT binding sites and conformational conversion depends upon the protein concentration. The HOI further undergoes structural rearrangement to form protofibrils in the "slow" step, which, consequently, assembles in the "very slow" step to form an amyloid-like assembly. The spectroscopic properties of the amyloid-like assembly across the protein concentration remain similar. Additionally, we observe no lag phase across protein concentration for all the probes studied, suggesting that the aggregation process follows a linear polymerization reaction. Overall, our study demonstrates that the amyloid-like assembly forms in multiple steps, which is also supported by the temperature dependence of the kinetics.
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Affiliation(s)
- Meenakshi Pillai
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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12
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Gao G, Liu X, Gu Z, Mu Q, Zhu G, Zhang T, Zhang C, Zhou L, Shen L, Sun T. Engineering Nanointerfaces of Au 25 Clusters for Chaperone-Mediated Peptide Amyloidosis. NANO LETTERS 2022; 22:2964-2970. [PMID: 35297644 DOI: 10.1021/acs.nanolett.2c00149] [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: 06/14/2023]
Abstract
Synthetic nanomaterials possessing biomolecular-chaperone functions are good candidates for modulating physicochemical interactions in many bioapplications. Despite extensive research, no general principle to engineer nanomaterial surfaces is available to precisely manipulate biomolecular conformations and behaviors, greatly limiting attempts to develop high-performance nanochaperone materials. Here, we demonstrate that, by quantifying the length (-SCxR±, x = 3-11) and charges (R- = -COO-, R+ = -NH3+) of ligands on Au25 gold nanochaperones (AuNCs), simulating binding sites and affinities of amyloid-like peptides with AuNCs, and probing peptide folding and fibrillation in the presence of AuNCs, it is possible to precisely manipulate the peptides' conformations and, thus, their amyloidosis via customizing AuNCs nanointerfaces. We show that intermediate-length liganded AuNCs with a specific charge chaperone peptides' native conformations and thus inhibit their fibrillation, while other types of AuNCs destabilize peptides and promote their fibrillation. We offer a microscopic molecular insight into peptide identity on AuNCs and provide a guideline in customizing nanochaperones via manipulating their nanointerfaces.
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Affiliation(s)
- Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Xinglin Liu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Zhenhua Gu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Qingxue Mu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Guowei Zhu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Ting Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Cheng Zhang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Lin Zhou
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Lei Shen
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| | - Taolei Sun
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
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13
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Rasmussen HØ, Otzen DE, Pedersen JS. Induction, inhibition, and incorporation: Different roles for anionic and zwitterionic lysolipids in the fibrillation of the functional amyloid FapC. J Biol Chem 2022; 298:101569. [PMID: 35007533 PMCID: PMC8888460 DOI: 10.1016/j.jbc.2022.101569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Amyloid proteins are widespread in nature both as pathological species involved in several diseases and as functional entities that can provide protection and storage for the organism. Lipids have been found in amyloid deposits from various amyloid diseases and have been shown to strongly affect the formation and structure of both pathological and functional amyloid proteins. Here, we investigate how fibrillation of the functional amyloid FapC from Pseudomonas is affected by two lysolipids, the zwitterionic lipid 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine and the anionic lipid 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1′-rac-glycerol) (LPG). Small-angle X-ray scattering, circular dichroism, dynamic light scattering, and thioflavin T fluorescence measurements were performed simultaneously on the same sample to ensure reproducibility and allow a multimethod integrated analysis. We found that LPG strongly induces fibrillation around its critical micelle concentration (cmc) by promoting formation of large structures, which mature via accumulation of intermediate fibril structures with a large cross section. At concentrations above its cmc, LPG strongly inhibits fibrillation by locking FapC in a core–shell complex. In contrast, lipid 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine induces fibrillation at concentrations above its cmc, not via strong interactions with FapC but by being incorporated during fibrillation and likely stabilizing the fibrillation nucleus to reduce the lag phase. Finally, we show that LPG is not incorporated into the fibril during assembly but rather can coat the final fibril. We conclude that lipids affect both the mechanism and outcome of fibrillation of functional amyloid, highlighting a role for lipid concentration and composition in the onset and mechanism of fibrillation in vivo.
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Affiliation(s)
- Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Gustav Wieds Vej 14, Aarhus University, 8000 Aarhus C, Denmark.
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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14
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Szała-Mendyk B, Molski A. Diverse Aggregation Kinetics Predicted by a Coarse-Grained Peptide Model. J Phys Chem B 2021; 125:7587-7597. [PMID: 34251838 PMCID: PMC8389928 DOI: 10.1021/acs.jpcb.1c00290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
![]()
Protein and peptide
aggregation is a ubiquitous phenomenon with
implications in medicine, pharmaceutical industry, and materials science.
An important issue in peptide aggregation is the molecular mechanism
of aggregate nucleation and growth. In many experimental studies,
sigmoidal kinetics curves show a clear lag phase ascribed to nucleation;
however, experimental studies also show downhill kinetics curves,
where the monomers decay continuously and no lag phase can be seen.
In this work, we study peptide aggregation kinetics using a coarse-grained
implicit solvent model introduced in our previous work. Our simulations
explore the hypothesis that the interplay between interchain attraction
and intrachain bending stiffness controls the aggregation kinetics
and transient aggregate morphologies. Indeed, our model reproduces
the aggregation modes seen in experiment: no observed aggregation,
nucleated aggregation, and rapid downhill aggregation. We find that
the interaction strength is the primary parameter determining the
aggregation mode, whereas the stiffness is a secondary parameter modulating
the transient morphologies and aggregation rates: more attractive
and stiff chains aggregate more rapidly and the transient morphologies
are more ordered. We also explore the effects of the initial monomer
concentration and the chain length. As the concentration decreases,
the aggregation mode shifts from downhill to nucleated and no-aggregation.
This concentration effect is in line with an experimental observation
that the transition between downhill and nucleated kinetics is concentration-dependent.
We find that longer peptides can aggregate at conditions where short
peptides do not aggregate at all. It supports an experimental observation
that the elongation of a homopeptide, e.g., polyglutamine, can increase
the aggregation propensity.
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Affiliation(s)
- Beata Szała-Mendyk
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89b, 61-614 Poznań, Poland
| | - Andrzej Molski
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Umultowska 89b, 61-614 Poznań, Poland
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15
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Morel B, Carrasco-Jiménez MP, Jurado S, Conejero-Lara F. Rapid Conversion of Amyloid-Beta 1-40 Oligomers to Mature Fibrils through a Self-Catalytic Bimolecular Process. Int J Mol Sci 2021; 22:ijms22126370. [PMID: 34198692 PMCID: PMC8232289 DOI: 10.3390/ijms22126370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022] Open
Abstract
The formation of fibrillar aggregates of the amyloid beta peptide (Aβ) in the brain is one of the hallmarks of Alzheimer’s disease (AD). A clear understanding of the different aggregation steps leading to fibrils formation is a keystone in therapeutics discovery. In a recent study, we showed that Aβ40 and Aβ42 form dynamic micellar aggregates above certain critical concentrations, which mediate a fast formation of more stable oligomers, which in the case of Aβ40 are able to evolve towards amyloid fibrils. Here, using different biophysical techniques we investigated the role of different fractions of the Aβ aggregation mixture in the nucleation and fibrillation steps. We show that both processes occur through bimolecular interplay between low molecular weight species (monomer and/or dimer) and larger oligomers. Moreover, we report here a novel self-catalytic mechanism of fibrillation of Aβ40, in which early oligomers generate and deliver low molecular weight amyloid nuclei, which then catalyze the rapid conversion of the oligomers to mature amyloid fibrils. This fibrillation catalytic activity is not present in freshly disaggregated low-molecular weight Aβ40 and is, therefore, a property acquired during the aggregation process. In contrast to Aβ40, we did not observe the same self-catalytic fibrillation in Aβ42 spheroidal oligomers, which could neither be induced to fibrillate by the Aβ40 nuclei. Our results reveal clearly that amyloid fibrillation is a multi-component process, in which dynamic collisions between different interacting species favor the kinetics of amyloid nucleation and growth.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
- Correspondence: (B.M.); (F.C.-L.); Tel.: +34-958-242-371 (F.C.-L.)
| | - María P. Carrasco-Jiménez
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
- Correspondence: (B.M.); (F.C.-L.); Tel.: +34-958-242-371 (F.C.-L.)
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16
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Soto-Ospina A, Araque Marín P, Bedoya G, Sepulveda-Falla D, Villegas Lanau A. Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer's Disease on the Orthosteric Site. Front Mol Biosci 2021; 8:649990. [PMID: 34150846 PMCID: PMC8206637 DOI: 10.3389/fmolb.2021.649990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease pathology is characterized by β-amyloid plaques and neurofibrillary tangles. Amyloid precursor protein is processed by β and γ secretase, resulting in the production of β-amyloid peptides with a length ranging from 38 to 43 amino acids. Presenilin 1 (PS1) is the catalytic unit of γ-secretase, and more than 200 PS1 pathogenic mutations have been identified as causative for Alzheimer's disease. A complete monocrystal structure of PS1 has not been determined so far due to the presence of two flexible domains. We have developed a complete structural model of PS1 using a computational approach with structure prediction software. Missing fragments Met1-Glut72 and Ser290-Glu375 were modeled and validated by their energetic and stereochemical characteristics. Then, with the complete structure of PS1, we defined that these fragments do not have a direct effect in the structure of the pore. Next, we used our hypothetical model for the analysis of the functional effects of PS1 mutations Ala246GLu, Leu248Pro, Leu248Arg, Leu250Val, Tyr256Ser, Ala260Val, and Val261Phe, localized in the catalytic pore. For this, we used a quantum mechanics/molecular mechanics (QM/MM) hybrid method, evaluating modifications in the topology, potential surface density, and electrostatic potential map of mutated PS1 proteins. We found that each mutation exerts changes resulting in structural modifications of the active site and in the shape of the pore. We suggest this as a valid approach for functional studies of PS1 in view of the possible impact in substrate processing and for the design of targeted therapeutic strategies.
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Affiliation(s)
- Alejandro Soto-Ospina
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- School of Life Sciences, Research and Innovation in Chemistry Formulations Group, EIA University, Envigado, Colombia
| | - Gabriel Bedoya
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
- Molecular Neuropathology of Alzheimer’s Disease, Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrés Villegas Lanau
- Faculty of Medicine, Group Molecular Genetics, University of Antioquia, Medellín, Colombia
- Faculty of Medicine, Group Neuroscience of Antioquia, University of Antioquia, Medellín, Colombia
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17
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Pittman JM, Srivastava AK, Boughter CT, Venkata BS, Zerweck J, Moore PC, Smok I, Tonelli M, Sachleben JR, Meredith SC. Nanodroplet Oligomers (NanDOs) of Aβ40. Biochemistry 2021; 60:2691-2703. [PMID: 34029056 DOI: 10.1021/acs.biochem.1c00147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Using atomic force microscopy (AFM) and nuclear magnetic resonance (NMR), we describe small Aβ40 oligomers, termed nanodroplet oligomers (NanDOs), which form rapidly and at Aβ40 concentrations too low for fibril formation. NanDOs were observed in putatively monomeric solutions of Aβ40 (e.g., by size exclusion chromatography). Video-rate scanning AFM shows rapid fusion and dissolution of small oligomer-sized particles, of which the median size increases with peptide concentration. In NMR (13C HSQC), a small number of chemical shifts changed with a change in peptide concentration. Paramagnetic relaxation enhancement NMR experiments also support the formation of NanDOs and suggest prominent interactions in hydrophobic domains of Aβ40. Addition of Zn2+ to Aβ40 solutions caused flocculation of NanDO-containing solutions, and selective loss of signal intensity in NMR spectra from residues in the N-terminal domain of Aβ40. NanDOs may represent the earliest aggregated form of Aβ40 in the aggregation pathway and are akin to premicelles in solutions of amphiphilies.
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Affiliation(s)
| | | | | | | | | | | | | | - Marco Tonelli
- NMR-FAM, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joseph R Sachleben
- NMR Core Facility, The University of Chicago, Chicago, Illinois 60637, United States
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18
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Guarrasi V, Rappa GC, Costa MA, Librizzi F, Raimondo M, Di Stefano V, Germanà MA, Vilasi S. Valorization of Apple Peels through the Study of the Effects on the Amyloid Aggregation Process of κ-Casein. Molecules 2021; 26:molecules26082371. [PMID: 33921801 PMCID: PMC8073991 DOI: 10.3390/molecules26082371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 01/13/2023] Open
Abstract
Waste valorization represents one of the main social challenges when promoting a circular economy and environmental sustainability. Here, we evaluated the effect of the polyphenols extracted from apple peels, normally disposed of as waste, on the amyloid aggregation process of κ-casein from bovine milk, a well-used amyloidogenic model system. The effect of the apple peel extract on protein aggregation was examined using a thioflavin T fluorescence assay, Congo red binding assay, circular dichroism, light scattering, and atomic force microscopy. We found that the phenolic extract from the peel of apples of the cultivar “Fuji”, cultivated in Sicily (Caltavuturo, Italy), inhibited κ-casein fibril formation in a dose-dependent way. In particular, we found that the extract significantly reduced the protein aggregation rate and inhibited the secondary structure reorganization that accompanies κ-casein amyloid formation. Protein-aggregated species resulting from the incubation of κ-casein in the presence of polyphenols under amyloid aggregation conditions were reduced in number and different in morphology.
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Affiliation(s)
- Valeria Guarrasi
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.C.R.); (M.A.C.); (F.L.); (M.R.); (S.V.)
- Correspondence: ; Tel.: +39-0916809356
| | - Giacoma Cinzia Rappa
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.C.R.); (M.A.C.); (F.L.); (M.R.); (S.V.)
| | - Maria Assunta Costa
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.C.R.); (M.A.C.); (F.L.); (M.R.); (S.V.)
| | - Fabio Librizzi
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.C.R.); (M.A.C.); (F.L.); (M.R.); (S.V.)
| | - Marco Raimondo
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.C.R.); (M.A.C.); (F.L.); (M.R.); (S.V.)
| | - Vita Di Stefano
- Dipartimento Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy;
| | - Maria Antonietta Germanà
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze Ed. 4, 90128 Palermo, Italy;
| | - Silvia Vilasi
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.C.R.); (M.A.C.); (F.L.); (M.R.); (S.V.)
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19
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Wu M, Dorosh L, Schmitt-Ulms G, Wille H, Stepanova M. Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations. PLoS Comput Biol 2021; 17:e1008771. [PMID: 33711010 PMCID: PMC7990313 DOI: 10.1371/journal.pcbi.1008771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/24/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14’s presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42–SST14, Aβ42–AVP, and Aβ40–SST14. The Aβ42–SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42–SST14 system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ42–SST14 oligomerization. Improper folding of proteins causes disorders known as protein misfolding diseases. Under normal conditions most proteins adopt particular folds, which allow them functioning properly. However, for reasons that are not yet fully understood, proteins may misfold and aggregate, forming deposits known as amyloid fibrils, which accumulate in the brain or other tissues. This process affects functioning of the nervous system, gradually causing loss of cognitive abilities. Alzheimer’s disease is one of the most common diseases from this group. A better understanding of the aggregation of peptides implicated in Alzheimer’s disease, known as amyloid beta (Aβ) peptides, may facilitate the development of treatments that ameliorate or prevent the disease. We use detailed molecular dynamics simulations to investigate the influence of somatostatin-14 (SST14), a cyclic neuropeptide that might be involved in the amyloidogenic aggregation of Aβ, on molecular processes occurring at the onset of Aβ aggregation. Results of these simulations explain how the presence of SST14 might alter pathways of aggregation of Aβ, shedding light upon the possible role of extrinsic factors in the aggregation at a molecular level.
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Affiliation(s)
- Min Wu
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada
- Centre for Prions and Protein Folding Diseases, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
- * E-mail:
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20
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Evidence of the existence of micellar-like aggregates for α-synuclein. Int J Biol Macromol 2021; 177:392-400. [PMID: 33631264 DOI: 10.1016/j.ijbiomac.2021.02.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/14/2021] [Accepted: 02/20/2021] [Indexed: 11/20/2022]
Abstract
We have been investigating the early stages of α-synuclein (Syn) aggregation, a small presynaptic protein implicated in Parkinson's disease. We previously reported that for pH jumps (1000 s) from pH 7 to pH 2 the variation of the Syn intrinsic fluorescence intensity did not change in the concentration range of ca. 10-50 μM (ref. 16). Additionally, I reported dynamic light scattering (DLS) experiments revealing the formation of early large Syn aggregates (ref. 7). These reported results mean that some molecular entity is being early formed. Herein, it was decided to investigate in detail these early Syn aggregates by using light scattering. By DLS analysis, these aggregates exhibited a hydrodynamic diameter of ca. 420 nm along with a high scattering intensity, characteristic of micellar-like aggregates formation. The critical micelle concentration (CMC) at which the Syn micellar-like aggregates are formed was ca. 10 μM. DLS analysis has also revealed that the micellar-like aggregates for Syn evolved, for protein concentrations >100 μM, to the formation of smaller aggregates (hydrodynamic diameter of ca. 165 nm), possibly Syn oligomers. The Syn micellar-like aggregates formed at pH 7 solutions seem to be active species and to have a role in this protein aggregation mechanism.
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21
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Wu T, Lai R, Yao C, Juang J, Lin S. Supramolecular Bait to Trigger Non-Equilibrium Co-Assembly and Clearance of Aβ42. Angew Chem Int Ed Engl 2021; 60:4014-4017. [PMID: 33191624 PMCID: PMC7898541 DOI: 10.1002/anie.202013754] [Citation(s) in RCA: 3] [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: 10/12/2020] [Indexed: 12/20/2022]
Abstract
In living systems, non-equilibrium states that control the assembly-disassembly of cellular components underlie the gradual complexification of life, whereas in nonliving systems, most molecules follow the laws of thermodynamic equilibrium to sustain dynamic consistency. Little is known about the roles of non-equilibrium states of interactions between supramolecules in living systems. Here, a non-equilibrium state of interaction between supramolecular lipopolysaccharide (LPS) and Aβ42, an aggregate-prone protein that causes Alzheimer's disease (AD), was identified. Structurally, Aβ42 presents a specific groove that is recognized by the amphiphilicity of LPS bait in a non-equilibrium manner. Functionally, the transient complex elicits a cellular response to clear extracellular Aβ42 deposits in neuronal cells. Since the impaired clearance of toxic Aβ42 deposits correlates with AD pathology, the non-equilibrium LPS and Aβ42 could represent a useful target for developing AD therapeutics.
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Affiliation(s)
- Te‐Haw Wu
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
| | - Rai‐Hua Lai
- Institute of Molecular and Genomic MedicineNHRITaiwan
| | - Chun‐Nien Yao
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
| | - Jyh‐Lyh Juang
- Institute of Molecular and Genomic MedicineNHRITaiwan
| | - Shu‐Yi Lin
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
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22
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Lau CYJ, Mastrobattista E. Programming supramolecular peptide materials by modulating the intermediate steps in the complex assembly pathway: Implications for biomedical applications. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2020.101396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Alberti S, Hyman AA. Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing. Nat Rev Mol Cell Biol 2021; 22:196-213. [PMID: 33510441 DOI: 10.1038/s41580-020-00326-6] [Citation(s) in RCA: 439] [Impact Index Per Article: 146.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
Abstract
Biomolecular condensates are membraneless intracellular assemblies that often form via liquid-liquid phase separation and have the ability to concentrate biopolymers. Research over the past 10 years has revealed that condensates play fundamental roles in cellular organization and physiology, and our understanding of the molecular principles, components and forces underlying their formation has substantially increased. Condensate assembly is tightly regulated in the intracellular environment, and failure to control condensate properties, formation and dissolution can lead to protein misfolding and aggregation, which are often the cause of ageing-associated diseases. In this Review, we describe the mechanisms and regulation of condensate assembly and dissolution, highlight recent advances in understanding the role of biomolecular condensates in ageing and disease, and discuss how cellular stress, ageing-related loss of homeostasis and a decline in protein quality control may contribute to the formation of aberrant, disease-causing condensates. Our improved understanding of condensate pathology provides a promising path for the treatment of protein aggregation diseases.
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Affiliation(s)
- Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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24
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Wu T, Lai R, Yao C, Juang J, Lin S. Supramolecular Bait to Trigger Non‐Equilibrium Co‐Assembly and Clearance of Aβ42. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202013754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Te‐Haw Wu
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
| | - Rai‐Hua Lai
- Institute of Molecular and Genomic Medicine NHRI Taiwan
| | - Chun‐Nien Yao
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
| | - Jyh‐Lyh Juang
- Institute of Molecular and Genomic Medicine NHRI Taiwan
| | - Shu‐Yi Lin
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
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25
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Ghosh P, De P. Modulation of Amyloid Protein Fibrillation by Synthetic Polymers: Recent Advances in the Context of Neurodegenerative Diseases. ACS APPLIED BIO MATERIALS 2020; 3:6598-6625. [DOI: 10.1021/acsabm.0c01021] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pooja Ghosh
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 Nadia, West Bengal, India
| | - Priyadarsi De
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 Nadia, West Bengal, India
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26
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Ruiz-Arias Á, Paredes JM, Di Biase C, Cuerva JM, Giron MD, Salto R, González-Vera JA, Orte A. Seeding and Growth of β-Amyloid Aggregates upon Interaction with Neuronal Cell Membranes. Int J Mol Sci 2020; 21:ijms21145035. [PMID: 32708806 PMCID: PMC7404110 DOI: 10.3390/ijms21145035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/22/2022] Open
Abstract
In recent years, the prevalence of amyloid neurodegenerative diseases such as Alzheimer's disease (AD) has significantly increased in developed countries due to increased life expectancy. This amyloid disease is characterized by the presence of accumulations and deposits of β-amyloid peptide (Aβ) in neuronal tissue, leading to the formation of oligomers, fibers, and plaques. First, oligomeric intermediates that arise during the aggregation process are currently thought to be primarily responsible for cytotoxicity in cells. This work aims to provide further insights into the mechanisms of cytotoxicity by studying the interaction of Aβ aggregates with Neuro-2a (N2a) neuronal cells and the effects caused by this interaction. For this purpose, we have exploited the advantages of advanced, multidimensional fluorescence microscopy techniques to determine whether different types of Aβ are involved in higher rates of cellular toxicity, and we measured the cellular stress caused by such aggregates by using a fluorogenic intracellular biothiol sensor. Stress provoked by the peptide is evident by N2a cells generating high levels of biothiols as a defense mechanism. In our study, we demonstrate that Aβ aggregates act as seeds for aggregate growth upon interacting with the cellular membrane, which results in cell permeability and damage and induces lysis. In parallel, these damaged cells undergo a significant increase in intracellular biothiol levels.
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Affiliation(s)
- Álvaro Ruiz-Arias
- Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus Cartuja, 18071 Granada, Spain; (Á.R.-A.); (J.M.P.); (C.D.B.); (J.A.G.-V.)
| | - Jose M. Paredes
- Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus Cartuja, 18071 Granada, Spain; (Á.R.-A.); (J.M.P.); (C.D.B.); (J.A.G.-V.)
| | - Chiara Di Biase
- Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus Cartuja, 18071 Granada, Spain; (Á.R.-A.); (J.M.P.); (C.D.B.); (J.A.G.-V.)
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Juan M. Cuerva
- Departamento de Química Orgánica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva, 18071 Granada, Spain;
| | - María D. Giron
- Departamento de Bioquímica y Biología Molecular II, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus Cartuja, 18071 Granada, Spain; (M.D.G.); (R.S.)
| | - Rafael Salto
- Departamento de Bioquímica y Biología Molecular II, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus Cartuja, 18071 Granada, Spain; (M.D.G.); (R.S.)
| | - Juan A. González-Vera
- Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus Cartuja, 18071 Granada, Spain; (Á.R.-A.); (J.M.P.); (C.D.B.); (J.A.G.-V.)
| | - Angel Orte
- Departamento de Fisicoquímica, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Farmacia, Universidad de Granada, Campus Cartuja, 18071 Granada, Spain; (Á.R.-A.); (J.M.P.); (C.D.B.); (J.A.G.-V.)
- Correspondence: ; Tel.: +34-958243825
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Abstract
The spontaneous assembly of proteins into amyloid fibrils is a phenomenon central to many increasingly common and currently incurable human disorders, including Alzheimer's and Parkinson's diseases. Oligomeric species form transiently during this process and not only act as essential intermediates in the assembly of new filaments but also represent major pathogenic agents in these diseases. While amyloid fibrils possess a common, defining set of physicochemical features, oligomers, by contrast, appear much more diverse, and their commonalities and differences have hitherto remained largely unexplored. Here, we use the framework of chemical kinetics to investigate their dynamical properties. By fitting experimental data for several unrelated amyloidogenic systems to newly derived mechanistic models, we find that oligomers present with a remarkably wide range of kinetic and thermodynamic stabilities but that they possess two properties that are generic: they are overwhelmingly nonfibrillar, and they predominantly dissociate back to monomers rather than maturing into fibrillar species. These discoveries change our understanding of the relationship between amyloid oligomers and amyloid fibrils and have important implications for the nature of their cellular toxicity.
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L. Almeida Z, M. M. Brito R. Structure and Aggregation Mechanisms in Amyloids. Molecules 2020; 25:molecules25051195. [PMID: 32155822 PMCID: PMC7179426 DOI: 10.3390/molecules25051195] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022] Open
Abstract
The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.
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Ma W, Tribet C, Guyot S, Zanchi D. Tannin-controlled micelles and fibrils of κ-casein. J Chem Phys 2020; 151:245103. [PMID: 31893889 DOI: 10.1063/1.5128057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Effects of green tea tannin epigallocatechin-gallate (EGCG) on thermal-stress-induced amyloid fibril formation of reduced carboxymethylated bovine milk protein κ-casein were studied by dynamical light scattering and small angle X-ray scattering (SAXS). Two populations of aggregates, micelles, and fibrils dominated the time evolution of light scattering intensity and of effective hydrodynamic diameter. SAXS experiments allowed us to resolve micelles and fibrils so that the time dependence of the scattering profile revealed the structural evolution of the two populations. The low-Q scattering intensity prior to an expected increase in time due to fibril growth shows an intriguing rapid decrease, which is interpreted as the release of monomers from micelles. This phenomenon, observed both in the absence and in the presence of EGCG, indicates that under thermal stress free conditions, native monomers are converted to amyloid-prone monomers that do not form micelles. The consumption of free native monomers results in a release of native monomers from micelles because only native proteins participate in micelle-monomer (quasi)equilibrium. This release is reversible, indicating also that native-to-amyloid-prone monomer conversion is reversible as well. We show that EGCG does not bind to protein in fibrils, neither does it affect/prevent the proamyloid conversion of monomers. EGCG hinders the addition of monomers to growing fibrils. These facts allowed us to propose the kinetics model for EGCG-controlled amyloid aggregation of micellar proteins. Therein, we introduced the growth-rate inhibition function, which quantitatively accounts for the effect of EGCG on the fibril growth at any degree of thermal stress.
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Affiliation(s)
- Wei Ma
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, F-75005 Paris, France
| | - Christophe Tribet
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, F-75005 Paris, France
| | - Sylvain Guyot
- INRA UR1268 BIA-Polyphenols, Reactivity, Processes, F-35653 Le Rheu, France
| | - Dražen Zanchi
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, F-75005 Paris, France
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Tonali N, Dodero VI, Kaffy J, Hericks L, Ongeri S, Sewald N. Real-Time BODIPY-Binding Assay To Screen Inhibitors of the Early Oligomerization Process of Aβ1-42 Peptide. Chembiochem 2020; 21:1129-1135. [PMID: 31702868 PMCID: PMC7217026 DOI: 10.1002/cbic.201900652] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Indexed: 01/03/2023]
Abstract
Misfolding and aggregation of amyloid β1–42 peptide (Aβ1–42) play a central role in the pathogenesis of Alzheimer's disease (AD). Targeting the highly cytotoxic oligomeric species formed during the early stages of the aggregation process represents a promising therapeutic strategy to reduce the toxicity associated with Aβ1–42. Currently, the thioflavin T (ThT) assay is the only established spectrofluorometric method to screen aggregation inhibitors. The success of the ThT assay is that it can detect Aβ1–42 aggregates with high β‐sheet content, such as protofibrils or fibrils, which appear in the late aggregation steps. Unfortunately, by using the ThT assay, the detection of inhibitors of early soluble oligomers that present a low β‐sheet character is challenging. Herein, a new, facile, and robust boron‐dipyrromethene (BODIPY) real‐time assay suitable for 96‐well plate format, which allows screening of compounds as selective inhibitors of the formation of Aβ1–42 oligomers, is reported. These inhibitors decrease the cellular toxicity of Aβ1–42, although they fail in the ThT assay. The findings have been confirmed and validated by structural analysis and cell viability assays under comparable experimental conditions. It is demonstrated that the BODIPY assay is a convenient method to screen and discover new candidate compounds that slow down or stop the pathological early oligomerization process and are active in the cellular assay. Therefore, it is a suitable complementary screening method of the current ThT assay.
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Affiliation(s)
- Nicolo Tonali
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany.,BioCIS, CNRS/Université Paris Sud, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry Cedex, France
| | - Veronica I Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany
| | - Julia Kaffy
- BioCIS, CNRS/Université Paris Sud, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry Cedex, France
| | - Loreen Hericks
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany
| | - Sandrine Ongeri
- BioCIS, CNRS/Université Paris Sud, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296, Châtenay-Malabry Cedex, France
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, P. O. Box 100131, 33501, Bielefeld, Germany
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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32
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Azouz M, Cullin C, Lecomte S, Lafleur M. Membrane domain modulation of Aβ 1-42 oligomer interactions with supported lipid bilayers: an atomic force microscopy investigation. NANOSCALE 2019; 11:20857-20867. [PMID: 31657431 DOI: 10.1039/c9nr06361g] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Alzheimer's disease is a devastating pathology affecting an increasing number of individuals following the general rise in life expectancy. Amyloid peptide Aβ1-42 has been identified as one of the main culprits of the disease. The peptide has been shown to have major effects on lipid membranes, including membrane fragmentation. The membrane composition has been identified as a factor that plays a pivotal role in regulating peptide/membrane interactions and several results suggest that lipid domains, or rafts, can promote peptide-induced membrane damage. In this work, we examined the effects of lipid segregation on the membrane-perturbing ability of Aβ1-42 and an oligomeric mutant (G37C), a peptide that shares common features with the suspected toxic intermediates involved in the neurodegeneration process. Atomic force microscopy (AFM) was used to determine the impact of these peptides on the supported lipid bilayers of various compositions. In 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phosphocholine/cholesterol (DOPC/DPPC/cholesterol) and DOPC/sphingomyelin/cholesterol ternary mixtures, two systems exhibiting liquid-liquid phase separations, it was shown that Aβ1-42 and G37C exclusively aggregated on liquid-disordered-phase domains, creating large deposits and even causing membrane fragmentation for the latter composition. Cholesterol and ganglioside GM1, the two most documented lipids in the context of Alzheimer's disease, are also considered to play a crucial role in promoting detrimental interactions with amyloid peptides. We show that, in model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes, the presence of either cholesterol or GM1 in a proportion of 10 mol%, a content supposed to lead to domain formation, favoured the association of both Aβ1-42 and G37C, leading to a harmful membrane fragmentation. The AFM results established that the presence of domains favoured membrane perturbations induced by the amyloid peptides. It is proposed that lipid packing defects at the domain interface could act as adsorption and nucleation sites for the amyloid peptides. The more extensive bilayer perturbations induced by G37C compared to Aβ1-42 supported this hypothesis, indicating that oligomers that cannot mature to the fibril state can present considerable toxicity.
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Affiliation(s)
- Mehdi Azouz
- Chimie et Biologie des Membranes et Nanoobjets, CBMN CNRS UMR 5248, Université de Bordeaux, Allée Geoffroy de Saint-Hilaire, 33600 Pessac, France and Department of Chemistry, Université de Montréal, Montréal, Québec, Canada.
| | - Christophe Cullin
- Chimie et Biologie des Membranes et Nanoobjets, CBMN CNRS UMR 5248, Université de Bordeaux, Allée Geoffroy de Saint-Hilaire, 33600 Pessac, France
| | - Sophie Lecomte
- Chimie et Biologie des Membranes et Nanoobjets, CBMN CNRS UMR 5248, Université de Bordeaux, Allée Geoffroy de Saint-Hilaire, 33600 Pessac, France
| | - Michel Lafleur
- Department of Chemistry, Université de Montréal, Montréal, Québec, Canada.
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Roy B, Govindaraju T. Amino Acids and Peptides as Functional Components in Arylenediimide-Based Molecular Architectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190215] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Bappaditya Roy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru-560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P. O., Bengaluru-560064, Karnataka, India
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Srivastava AK, Pittman JM, Zerweck J, Venkata BS, Moore PC, Sachleben JR, Meredith SC. β-Amyloid aggregation and heterogeneous nucleation. Protein Sci 2019; 28:1567-1581. [PMID: 31276610 PMCID: PMC6699094 DOI: 10.1002/pro.3674] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 01/09/2023]
Abstract
In this article, we consider the role of heterogeneous nucleation in β-amyloid aggregation. Heterogeneous nucleation is more common and occurs at lower levels of supersaturation than homogeneous nucleation. The nucleation period is also the stage at which most of the polymorphism of amyloids arises, this being one of the defining features of amyloids. We focus on several well-known heterogeneous nucleators of β-amyloid, including lipid surfaces, especially those enriched in gangliosides and cholesterol, and divalent metal ions. These two broad classes of nucleators affect β-amyloid particularly in light of the amphiphilicity of these peptides: the N-terminal region, which is largely polar and charged, contains the metal binding site, whereas the C-terminal region is aliphatic and is important in lipid binding. Notably, these two classes of nucleators can interact cooperatively, aggregation begetting greater aggregation.
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Affiliation(s)
- Atul K. Srivastava
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | - Jay M. Pittman
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | - Jonathan Zerweck
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | - Bharat S. Venkata
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
| | | | | | - Stephen C. Meredith
- Department of PathologyThe University of ChicagoChicagoIllinois
- Department of Biochemistry and Molecular BiologyThe University of ChicagoChicagoIllinois
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Lee J, Lee JH, Paik SR, Yeom B, Char K. Thermally triggered self-assembly of κ-casein amyloid nanofibrils and their nanomechanical properties. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.121626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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36
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Morel B, Conejero-Lara F. Early mechanisms of amyloid fibril nucleation in model and disease-related proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140264. [PMID: 31437584 DOI: 10.1016/j.bbapap.2019.140264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/18/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
Protein amyloid aggregation is a hallmark in neuropathologies and other diseases of tremendous impact such as Alzheimer's or Parkinson's diseases. During the last decade, it has become increasingly evident that neuronal death is mainly induced by proteinaceous oligomers rather than the mature amyloid fibrils. Therefore, the earliest molecular events occurring during the amyloid aggregation cascade represent a growing interest of study. Important breakthroughs have been achieved using experimental data from different proteins, used as models, as well as systems related to diseases. Here, we summarize the structural properties of amyloid oligomeric and fibrillar aggregates and review the recent advances on how biophysical techniques can be combined with quantitative kinetic analysis and theoretical models to study the detailed mechanism of oligomer formation and nucleation of fibrils. These insights into the mechanism of early oligomerization and amyloid nucleation are of relevant interest in drug discovery and in the design of preventive strategies against neurodegenerative diseases.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain.
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain
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