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Wang Y, Liao Y, Zhang YJ, Wu XH, Qiao ZY, Wang H. Self-Assembled Peptide with Morphological Structure for Bioapplication. Biomacromolecules 2024; 25:6367-6394. [PMID: 39297513 DOI: 10.1021/acs.biomac.4c01179] [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: 10/15/2024]
Abstract
Peptide materials, such as self-assembled peptide materials, are very important biomaterials. Driven by multiple interaction forces, peptide molecules can self-assemble into a variety of different macroscopic forms with different properties and functions. In recent years, the research on self-assembled peptides has made great progress from laboratory design to clinical application. This review focuses on the different morphologies, including nanoparticles, nanovesicles, nanotubes, nanofibers, and others, formed by self-assembled peptide. The mechanisms and applications of the morphology transformation are also discussed in this paper, and the future direction of self-assembled nanomaterials is envisioned.
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Affiliation(s)
- Yu Wang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Yusi Liao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, P. R. China
| | - Ying-Jin Zhang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Xiu-Hai Wu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
- Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin150081, P. R. China
| | - Zeng-Ying Qiao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Hao Wang
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450052, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No.11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, P. R. China
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2
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Li Y, Awasthi S, Bryan L, Ehrlich RS, Tonali N, Balog S, Yang J, Sewald N, Mayer M. Fluorescence-Based Monitoring of Early-Stage Aggregation of Amyloid-β, Amylin Peptide, Tau, and α-Synuclein Proteins. ACS Chem Neurosci 2024; 15:3113-3123. [PMID: 39150403 PMCID: PMC11378287 DOI: 10.1021/acschemneuro.4c00097] [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: 08/17/2024] Open
Abstract
Early-stage aggregates of amyloid-forming proteins, specifically soluble oligomers, are implicated in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. Protein aggregation is typically monitored by fluorescence using the amyloid-binding fluorophore thioflavin T (ThT). Thioflavin T interacts, however, preferentially with fibrillar amyloid structures rather than with soluble, early-stage aggregates. In contrast, the two fluorophores, aminonaphthalene 2-cyanoacrylate-spiropyran (AN-SP) and triazole-containing boron-dipyrromethene (taBODIPY), were reported to bind preferentially to early-stage aggregates of amyloidogenic proteins. The present study compares ThT with AN-SP and taBODIPY with regard to their ability to monitor early stages of aggregation of four different amyloid-forming proteins, including amyloid-β (Aβ), tau protein, amylin, and α-synuclein. The results show that the three fluorophores vary in their suitability to monitor the early aggregation of different amyloid-forming proteins. For instance, in the presence of Aβ and amylin, the fluorescence intensity of AN-SP increased at an earlier stage of aggregation than the fluorescence of ThT, albeit with only a small fluorescence increase in the case of AN-SP. In contrast, in the presence of tau and amylin, the fluorescence intensity of taBODIPY increased at an earlier stage of aggregation than the fluorescence of ThT. Finally, α-synuclein aggregation could only be monitored by ThT fluorescence; neither AN-SP nor taBODIPY showed a significant increase in fluorescence over the course of aggregation of α-synuclein. These results demonstrate the ability of AN-SP and taBODIPY to monitor the formation of early-stage aggregates from specific amyloid-forming proteins at an early stage of aggregation, although moderate increases in fluorescence intensity, relatively large uncertainties in fluorescence values, and limited solubility of both fluorophores limit their usefulness for some amyloid proteins. The capability to monitor early aggregation of some amyloid proteins, such as amylin, might accelerate the discovery of aggregation inhibitors to minimize the formation of toxic oligomeric species for potential therapeutic use.
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Affiliation(s)
- Yuanjie Li
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
| | - Saurabh Awasthi
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Raebareli (NIPER-R), Lucknow, Uttar Pradesh 226002, India
| | - Louise Bryan
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
| | - Rachel S Ehrlich
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Nicolo Tonali
- CNRS, BioCIS, Bâtiment Henri Moissan, Université Paris-Saclay, 17 Av. des Sciences, Orsay 91400, France
| | - Sandor Balog
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0358, United States
| | - Norbert Sewald
- Bielefeld University, Department of Chemistry P.O. Box 100131, Bielefeld 33501, Germany
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
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3
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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4
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Chia S, Faidon Brotzakis Z, Horne RI, Possenti A, Mannini B, Cataldi R, Nowinska M, Staats R, Linse S, Knowles TPJ, Habchi J, Vendruscolo M. Structure-Based Discovery of Small-Molecule Inhibitors of the Autocatalytic Proliferation of α-Synuclein Aggregates. Mol Pharm 2023; 20:183-193. [PMID: 36374974 PMCID: PMC9811465 DOI: 10.1021/acs.molpharmaceut.2c00548] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/15/2022]
Abstract
The presence of amyloid fibrils of α-synuclein is closely associated with Parkinson's disease and related synucleinopathies. It is still very challenging, however, to systematically discover small molecules that prevent the formation of these aberrant aggregates. Here, we describe a structure-based approach to identify small molecules that specifically inhibit the surface-catalyzed secondary nucleation step in the aggregation of α-synuclein by binding to the surface of the amyloid fibrils. The resulting small molecules are screened using a range of kinetic and thermodynamic assays for their ability to bind α-synuclein fibrils and prevent the further generation of α-synuclein oligomers. This study demonstrates that the combination of structure-based and kinetic-based drug discovery methods can lead to the identification of small molecules that selectively inhibit the autocatalytic proliferation of α-synuclein aggregates.
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Affiliation(s)
- Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Z. Faidon Brotzakis
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Robert I. Horne
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Andrea Possenti
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Benedetta Mannini
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Rodrigo Cataldi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Magdalena Nowinska
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Roxine Staats
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Sara Linse
- Department
of Biochemistry & Structural Biology, Center for Molecular Protein
Science, Lund University, 221 00Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
- Department
of Physics, Cavendish Laboratory, CambridgeCB3 0HE, U.K.
| | - Johnny Habchi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
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5
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Uddin A, Malla JA, Kumar H, Kumari M, Sinha S, Sharma VK, Kumar Y, Talukdar P, Lahiri M, Maiti TK, Hazra P. Development of a Systematic Strategy toward Promotion of α-Synuclein Aggregation Using 2-Hydroxyisophthalamide-Based Systems. Biochemistry 2022; 61:2267-2279. [PMID: 36219819 DOI: 10.1021/acs.biochem.2c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Establishing a potent scheme against α-synuclein aggregation involved in Parkinson's disease has been evaluated as a promising route to identify compounds that either inhibit or promote the aggregation process of α-synuclein. In the last two decades, this perspective has guided a dramatic increase in the efforts, focused on developing potent drugs either for retardation or promotion of the self-assembly process of α-synuclein. To address this issue, using a chemical kinetics platform, we developed a strategy that enabled a progressively detailed analysis of the molecular events leading to protein aggregation at the microscopic level in the presence of a recently synthesized 2-hydroxyisophthalamide class of small organic molecules based on their binding affinity. Furthermore, qualitatively, we have developed a strategy of disintegration of α-synuclein fibrils in the presence of these organic molecules. Finally, we have shown that these organic molecules effectively suppress the toxicity of α-synuclein oligomers in neuron cells.
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Affiliation(s)
- Aslam Uddin
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Javid Ahmad Malla
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Harish Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Manisha Kumari
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad121001, India
| | - Suman Sinha
- Institute of Pharmaceutical Research, GLA University, Mathura281406, India
| | - Virender Kumar Sharma
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Yashwant Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India.,National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru560065, India
| | - Pinaki Talukdar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Mayurika Lahiri
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
| | - Tushar Kanti Maiti
- Functional Proteomics Laboratory, Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, Faridabad121001, India
| | - Partha Hazra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune411008, Maharashtra, India
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6
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Almuslehi MSM, Sen MK, Shortland PJ, Mahns DA, Coorssen JR. Histological and Top-Down Proteomic Analyses of the Visual Pathway in the Cuprizone Demyelination Model. J Mol Neurosci 2022; 72:1374-1401. [PMID: 35644788 PMCID: PMC9170674 DOI: 10.1007/s12031-022-01997-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/07/2022] [Indexed: 10/27/2022]
Abstract
Abstract
A change in visual perception is a frequent early symptom of multiple sclerosis (MS), the pathoaetiology of which remains unclear. Following a slow demyelination process caused by 12 weeks of low-dose (0.1%) cuprizone (CPZ) consumption, histology and proteomics were used to investigate components of the visual pathway in young adult mice. Histological investigation did not identify demyelination or gliosis in the optic tracts, pretectal nuclei, superior colliculi, lateral geniculate nuclei or visual cortices. However, top-down proteomic assessment of the optic nerve/tract revealed a significant change in the abundance of 34 spots in high-resolution two-dimensional (2D) gels. Subsequent liquid chromatography-tandem mass spectrometry (LC-TMS) analysis identified alterations in 75 proteoforms. Literature mining revealed the relevance of these proteoforms in terms of proteins previously implicated in animal models, eye diseases and human MS. Importantly, 24 proteoforms were not previously described in any animal models of MS, eye diseases or MS itself. Bioinformatic analysis indicated involvement of these proteoforms in cytoskeleton organization, metabolic dysregulation, protein aggregation and axonal support. Collectively, these results indicate that continuous CPZ-feeding, which evokes a slow demyelination, results in proteomic changes that precede any clear histological changes in the visual pathway and that these proteoforms may be potential early markers of degenerative demyelinating conditions.
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7
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Blanco MA. Computational models for studying physical instabilities in high concentration biotherapeutic formulations. MAbs 2022; 14:2044744. [PMID: 35282775 PMCID: PMC8928847 DOI: 10.1080/19420862.2022.2044744] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Computational prediction of the behavior of concentrated protein solutions is particularly advantageous in early development stages of biotherapeutics when material availability is limited and a large set of formulation conditions needs to be explored. This review provides an overview of the different computational paradigms that have been successfully used in modeling undesirable physical behaviors of protein solutions with a particular emphasis on high-concentration drug formulations. This includes models ranging from all-atom simulations, coarse-grained representations to macro-scale mathematical descriptions used to study physical instability phenomena of protein solutions such as aggregation, elevated viscosity, and phase separation. These models are compared and summarized in the context of the physical processes and their underlying assumptions and limitations. A detailed analysis is also given for identifying protein interaction processes that are explicitly or implicitly considered in the different modeling approaches and particularly their relations to various formulation parameters. Lastly, many of the shortcomings of existing computational models are discussed, providing perspectives and possible directions toward an efficient computational framework for designing effective protein formulations.
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Affiliation(s)
- Marco A. Blanco
- Materials and Biophysical Characterization, Analytical R & D, Merck & Co., Inc, Kenilworth, NJ USA
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8
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The curvature of gold nanoparticles influences the exposure of amyloid-β and modulates its aggregation process. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 128:112269. [PMID: 34474828 DOI: 10.1016/j.msec.2021.112269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/09/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2022]
Abstract
Gold nanoparticles (GNP) are tunable nanomaterials that can be used to develop rational therapeutic inhibitors against the formation of pathological aggregates of proteins. In the case of the pathological aggregation of the amyloid-β protein (Aβ), the shape of the GNP can slow down or accelerate its aggregation kinetics. However, there is a lack of elementary knowledge about how the curvature of GNP alters the interaction with the Aβ peptide and how this interaction modifies key molecular steps of fibril formation. In this study, we analysed the effect of flat gold nanoprisms (GNPr) and curved gold nanospheres (GNS) on in vitro Aβ42 fibril formation kinetics by using the thioflavin-based kinetic assay and global fitting analysis, with several models of aggregation. Whereas GNPr accelerate the aggregation process and maintain the molecular mechanism of aggregation, GNS slow down this process and modify the molecular mechanism to one of fragmentation/secondary nucleation, with respect to controls. These results can be explained by a differential interaction between the Aβ peptide and GNP observed by Raman spectroscopy. While flat GNPr expose key hydrophobic residues involved in the Aβ peptide aggregation, curved GNS hide these residues from the solvent. Thus, this study provides mechanistic insights to improve the rational design of GNP nanomaterials for biomedical applications in the field of amyloid-related aggregation.
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9
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Torres KM, Delgado AS, Serrano ER, Falcón-Cruz NV, Meléndez A, Ramos I, Du D, Oyola R. Gallium nanoparticles as novel inhibitors of Aβ40 aggregation. MATERIALS ADVANCES 2021; 2:5471-5478. [PMID: 34458846 PMCID: PMC8366391 DOI: 10.1039/d1ma00461a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Alzheimer's disease (AD) has been consistently related to the formation of senile amyloid plaques mainly composed of amyloid β (Aβ) peptides. The toxicity of Aβ aggregates has been indicated to be responsible for AD pathology. One scenario to decrease Aβ toxicity is the development of effective inhibitors against Aβ amyloid formation. In this study, we investigate the effect of gallium nitride nanoparticles (GaN NPs) as inhibitors of Aβ40 amyloid formation using a combination of biophysical approaches. Our results show that the lag phase of Aβ40 aggregation kinetics is significantly retarded by GaN NPs in a concentration dependent manner, implying the activity of GaN NPs in interfering with the formation of the crucial nucleus during Aβ aggregation. Our results also show that GaN NPs can reduce the amyloid fibril elongation rate in the course of the aggregation kinetics. It is speculated that the high polarization characteristics of GaN NPs may provoke a strong interaction between the particles and Aβ40 peptide and in this way decrease self-association of the peptide monomers to form amyloids.
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Affiliation(s)
- Kyabeth M Torres
- University of Puerto Rico-Humacao, Department of Biology, Call Box 860 Humacao 00792 PR USA
| | - Ambar S Delgado
- University of Puerto Rico-Humacao, Department of Biology, Call Box 860 Humacao 00792 PR USA
| | - Erika R Serrano
- University of Puerto Rico-Humacao, Department of Chemistry, Call Box 860 Humacao 00792 PR USA
| | - Nitza V Falcón-Cruz
- University of Puerto Rico-Humacao, Department of Chemistry, Call Box 860 Humacao 00792 PR USA
| | - Anamaris Meléndez
- University of Puerto Rico-Humacao, Department of Physics & Electronics, Call Box 860 Humacao 00792 PR USA
| | - Idalia Ramos
- University of Puerto Rico-Humacao, Department of Physics & Electronics, Call Box 860 Humacao 00792 PR USA
| | - Deguo Du
- Florida Atlantic University, Department of Chemistry & Biochemistry Boca Raton 33431 FL USA
| | - Rolando Oyola
- University of Puerto Rico-Humacao, Department of Chemistry, Call Box 860 Humacao 00792 PR USA
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10
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Rice LJ, Ecroyd H, van Oijen AM. Illuminating amyloid fibrils: Fluorescence-based single-molecule approaches. Comput Struct Biotechnol J 2021; 19:4711-4724. [PMID: 34504664 PMCID: PMC8405898 DOI: 10.1016/j.csbj.2021.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022] Open
Abstract
The aggregation of proteins into insoluble filamentous amyloid fibrils is a pathological hallmark of neurodegenerative diseases that include Parkinson's disease and Alzheimer's disease. Since the identification of amyloid fibrils and their association with disease, there has been much work to describe the process by which fibrils form and interact with other proteins. However, due to the dynamic nature of fibril formation and the transient and heterogeneous nature of the intermediates produced, it can be challenging to examine these processes using techniques that rely on traditional ensemble-based measurements. Single-molecule approaches overcome these limitations as rare and short-lived species within a population can be individually studied. Fluorescence-based single-molecule methods have proven to be particularly useful for the study of amyloid fibril formation. In this review, we discuss the use of different experimental single-molecule fluorescence microscopy approaches to study amyloid fibrils and their interaction with other proteins, in particular molecular chaperones. We highlight the mechanistic insights these single-molecule techniques have already provided in our understanding of how fibrils form, and comment on their potential future use in studying amyloid fibrils and their intermediates.
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Affiliation(s)
- Lauren J. Rice
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Heath Ecroyd
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Antoine M. van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
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11
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Proteomics of Multiple Sclerosis: Inherent Issues in Defining the Pathoetiology and Identifying (Early) Biomarkers. Int J Mol Sci 2021; 22:ijms22147377. [PMID: 34298997 PMCID: PMC8306353 DOI: 10.3390/ijms22147377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple Sclerosis (MS) is a demyelinating disease of the human central nervous system having an unconfirmed pathoetiology. Although animal models are used to mimic the pathology and clinical symptoms, no single model successfully replicates the full complexity of MS from its initial clinical identification through disease progression. Most importantly, a lack of preclinical biomarkers is hampering the earliest possible diagnosis and treatment. Notably, the development of rationally targeted therapeutics enabling pre-emptive treatment to halt the disease is also delayed without such biomarkers. Using literature mining and bioinformatic analyses, this review assessed the available proteomic studies of MS patients and animal models to discern (1) whether the models effectively mimic MS; and (2) whether reasonable biomarker candidates have been identified. The implication and necessity of assessing proteoforms and the critical importance of this to identifying rational biomarkers are discussed. Moreover, the challenges of using different proteomic analytical approaches and biological samples are also addressed.
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12
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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; 22:6370. [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] [Grants] [Track Full Text] [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
| | - 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
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13
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Allosteric control of hemoglobin S fiber formation by oxygen and its relation to the pathophysiology of sickle cell disease. Proc Natl Acad Sci U S A 2020; 117:15018-15027. [PMID: 32527859 PMCID: PMC7334536 DOI: 10.1073/pnas.1922004117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The pathology of sickle cell disease is caused by polymerization of the abnormal hemoglobin S upon deoxygenation in the tissues to form fibers in red cells, causing them to deform and occlude the circulation. Drugs that allosterically shift the quaternary equilibrium from the polymerizing T quaternary structure to the nonpolymerizing R quaternary structure are now being developed. Here we update our understanding on the allosteric control of fiber formation at equilibrium by showing how the simplest extension of the classic quaternary two-state allosteric model of Monod, Wyman, and Changeux to include tertiary conformational changes provides a better quantitative description. We also show that if fiber formation is at equilibrium in vivo, the vast majority of cells in most tissues would contain fibers, indicating that it is unlikely that the disease would be survivable once the nonpolymerizing fetal hemoglobin has been replaced by adult hemoglobin S at about 1 y after birth. Calculations of sickling times, based on a recently discovered universal relation between the delay time prior to fiber formation and supersaturation, show that in vivo fiber formation is very far from equilibrium. Our analysis indicates that patients survive because the delay period allows the majority of cells to escape the small vessels of the tissues before fibers form. The enormous sensitivity of the duration of the delay period to intracellular hemoglobin composition also explains why sickle trait, the heterozygous condition, and the compound heterozygous condition of hemoglobin S with pancellular hereditary persistence of fetal hemoglobin are both relatively benign conditions.
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14
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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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15
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Eaton WA. Hemoglobin S polymerization and sickle cell disease: A retrospective on the occasion of the 70th anniversary of Pauling's Science paper. Am J Hematol 2020; 95:205-211. [PMID: 31763707 PMCID: PMC7003899 DOI: 10.1002/ajh.25687] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022]
Abstract
70 years ago, Linus Pauling, the legendary genius of 20th century chemistry, published his famous work on the molecular cause of sickle cell disease, a paper that gave birth to what is now called molecular medicine. In this paper, Pauling left important questions unanswered that have motivated an enormous amount of scientific and clinical research since then. This retrospective discusses the basic science studies that have answered those questions directly related to the kinetics and thermodynamics of hemoglobin S polymerization.
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Affiliation(s)
- William A. Eaton
- Laboratory of Chemical PhysicsNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland
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16
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Yang F, Zhang W, Jiang Y, Yin F, Han W, Li Z. Targeting the Amyloid-β Fibril Surface with a Constrained Helical Peptide Inhibitor. Biochemistry 2020; 59:290-296. [PMID: 31702899 DOI: 10.1021/acs.biochem.9b00800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-β (Aβ) oligomers are well-known toxic molecular species associated with Alzheimer's disease. Recent discoveries of the ability of amyloid fibril surfaces to convert soluble proteins into toxic oligomers suggested that these surfaces could serve as therapeutic targets for intervention. We have shown previously that a short helical peptide could be a key structural motif that can specifically recognize the K16-E22 region of the Aβ40 fibril surface with an affinity at the level of several micromolar. Here, we demonstrate that in-tether chiral center-induced helical stabilized peptides could also recognize the fibril surfaces, effectively inhibiting the surface-mediated oligomerization of Aβ40. Moreover, through extensive computational sampling, we observed two distinct ways in which the peptide inhibitors recognize the fibril surface. Apart from a binding mode that, in accord with the original design, involves hydrophobic side chains at the binding interface, we observed much more frequently another binding mode in which the hydrophobic staple interacts directly with the fibril surface. The affinity of the peptides for the fibril surface could be adjusted by tuning the hydrophobicity of the staple. The best candidate investigated here exhibits a submicromolar affinity (∼0.75 μM). Collectively, this work opens an avenue for the rational design of candidate drugs with stapled peptides for amyloid-related disease.
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Affiliation(s)
- Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Wan Zhang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Yixiang Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China.,Shenzhen Bay Laboratory , Shenzhen 518055 , China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China.,Shenzhen Bay Laboratory , Shenzhen 518055 , China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China.,Shenzhen Bay Laboratory , Shenzhen 518055 , China
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17
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Abstract
This work provides a clearer picture for non-classical nucleation by revealing the presence of various intermediates using advanced characterization techniques.
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Affiliation(s)
- Biao Jin
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
- Department of Chemistry
| | - Zhaoming Liu
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
| | - Ruikang Tang
- Department of Chemistry
- Zhejiang University
- Hangzhou
- China
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18
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Computational studies of protein aggregation mediated by amyloid: Fibril elongation and secondary nucleation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:461-504. [DOI: 10.1016/bs.pmbts.2019.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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19
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Suppression of the Peripheral Immune System Limits the Central Immune Response Following Cuprizone-Feeding: Relevance to Modelling Multiple Sclerosis. Cells 2019; 8:cells8111314. [PMID: 31653054 PMCID: PMC6912385 DOI: 10.3390/cells8111314] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023] Open
Abstract
Cuprizone (CPZ) preferentially affects oligodendrocytes (OLG), resulting in demyelination. To investigate whether central oligodendrocytosis and gliosis triggered an adaptive immune response, the impact of combining a standard (0.2%) or low (0.1%) dose of ingested CPZ with disruption of the blood brain barrier (BBB), using pertussis toxin (PT), was assessed in mice. 0.2% CPZ(±PT) for 5 weeks produced oligodendrocytosis, demyelination and gliosis plus marked splenic atrophy (37%) and reduced levels of CD4 (44%) and CD8 (61%). Conversely, 0.1% CPZ(±PT) produced a similar oligodendrocytosis, demyelination and gliosis but a smaller reduction in splenic CD4 (11%) and CD8 (14%) levels and no splenic atrophy. Long-term feeding of 0.1% CPZ(±PT) for 12 weeks produced similar reductions in CD4 (27%) and CD8 (43%), as well as splenic atrophy (33%), as seen with 0.2% CPZ(±PT) for 5 weeks. Collectively, these results suggest that 0.1% CPZ for 5 weeks may be a more promising model to study the ‘inside-out’ theory of Multiple Sclerosis (MS). However, neither CD4 nor CD8 were detected in the brain in CPZ±PT groups, indicating that CPZ-mediated suppression of peripheral immune organs is a major impediment to studying the ‘inside-out’ role of the adaptive immune system in this model over long time periods. Notably, CPZ(±PT)-feeding induced changes in the brain proteome related to the suppression of immune function, cellular metabolism, synaptic function and cellular structure/organization, indicating that demyelinating conditions, such as MS, can be initiated in the absence of adaptive immune system involvement.
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20
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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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21
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Jiang Y, Jiang X, Shi X, Yang F, Cao Y, Qin X, Hou Z, Xie M, Liu N, Fang Q, Yin F, Han W, Li Z. α-Helical Motif as Inhibitors of Toxic Amyloid-β Oligomer Generation via Highly Specific Recognition of Amyloid Surface. iScience 2019; 17:87-100. [PMID: 31255986 PMCID: PMC6606958 DOI: 10.1016/j.isci.2019.06.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/10/2019] [Accepted: 06/12/2019] [Indexed: 11/15/2022] Open
Abstract
Amyloid fibril surfaces can convert soluble proteins into toxic oligomers and are attractive targets for intervention of protein aggregation diseases. Thus far, molecules identified with inhibitory activity are either large proteins or flat cyclic compounds lacking in specificity. The main design difficulty is flatness of amyloid surfaces and the lack of knowledge on binding interfaces. Here, we demonstrate, for the first time, a rational design of alpha-helical peptide inhibitors targeting the amyloid-beta 40 (Aβ40) fibril surfaces, based on our in silico finding that a helical fragment of Aβ40 interacts in a unique way with side-chain arrays on the fibril surface. We strengthen the fragment's binding capability through mutations and helicity enhancement with our Terminal Aspartic acid strategy. The resulting inhibitor shows micromolar affinity for the fibril surface, effectively impedes the surface-mediated oligomerization of Aβ40, and mitigates its cytotoxicity. This work opens up an avenue to designing aggregation modulators for amyloid diseases.
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Affiliation(s)
- Yixiang Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China; Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Xuehan Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Xiaodong Shi
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Yang Cao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Xuan Qin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Mingsheng Xie
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Na Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Qi Fang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China; Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China.
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen 518055, China; Shenzhen Bay Laboratory, Shenzhen 518055, China.
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22
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Weber C, Michaels T, Mahadevan L. Spatial control of irreversible protein aggregation. eLife 2019; 8:e42315. [PMID: 31084715 PMCID: PMC6516824 DOI: 10.7554/elife.42315] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/01/2019] [Indexed: 12/19/2022] Open
Abstract
Liquid cellular compartments form in the cyto- or nucleoplasm and can regulate aberrant protein aggregation. Yet, the mechanisms by which these compartments affect protein aggregation remain unknown. Here, we combine kinetic theory of protein aggregation and liquid-liquid phase separation to study the spatial control of irreversible protein aggregation in the presence of liquid compartments. We find that even for weak interactions aggregates strongly partition into the liquid compartment. Aggregate partitioning is caused by a positive feedback mechanism of aggregate nucleation and growth driven by a flux maintaining the phase equilibrium between the compartment and its surrounding. Our model establishes a link between specific aggregating systems and the physical conditions maximizing aggregate partitioning into the compartment. The underlying mechanism of aggregate partitioning could be used to confine cytotoxic protein aggregates inside droplet-like compartments but may also represent a common mechanism to spatially control irreversible chemical reactions in general.
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Affiliation(s)
- Christoph Weber
- School of Engineering and Applied SciencesHarvard UniversityCambridgeUnited States
| | - Thomas Michaels
- School of Engineering and Applied SciencesHarvard UniversityCambridgeUnited States
| | - L Mahadevan
- Department of PhysicsHarvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
- Kavli Institute for NanoBio Science and TechnologyHarvard UniversityCambridgeUnited States
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23
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Ruggeri FS, Šneideris T, Vendruscolo M, Knowles TPJ. Atomic force microscopy for single molecule characterisation of protein aggregation. Arch Biochem Biophys 2019; 664:134-148. [PMID: 30742801 PMCID: PMC6420408 DOI: 10.1016/j.abb.2019.02.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The development of atomic force microscopy (AFM) has opened up a wide range of novel opportunities in nanoscience and new modalities of observation in complex biological systems. AFM imaging has been widely employed to resolve the complex and heterogeneous conformational states involved in protein aggregation at the single molecule scale and shed light onto the molecular basis of a variety of human pathologies, including neurodegenerative disorders. The study of individual macromolecules at nanoscale, however, remains challenging, especially when fully quantitative information is required. In this review, we first discuss the principles of AFM with a special emphasis on the fundamental factors defining its sensitivity and accuracy. We then review the fundamental parameters and approaches to work at the limit of AFM resolution in order to perform single molecule statistical analysis of biomolecules and nanoscale protein aggregates. This single molecule statistical approach has proved to be powerful to unravel the molecular and hierarchical assembly of the misfolded species present transiently during protein aggregation, to visualise their dynamics at the nanoscale, as well to study the structural properties of amyloid-inspired functional nanomaterials.
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Affiliation(s)
- Francesco Simone Ruggeri
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom.
| | - Tomas Šneideris
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Michele Vendruscolo
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom; Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, United Kingdom.
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24
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α-Synuclein misfolding and aggregation: Implications in Parkinson's disease pathogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:890-908. [PMID: 30853581 DOI: 10.1016/j.bbapap.2019.03.001] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/03/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
Abstract
α-Synuclein (α-Syn) has been extensively studied for its structural and biophysical properties owing to its pathophysiological role in Parkinson's disease (PD). Lewy bodies and Lewy neurites are the pathological hallmarks of PD and contain α-Syn aggregates as their major component. It was therefore hypothesized that α-Syn aggregation is actively associated with PD pathogenesis. The central role of α-Syn aggregation in PD is further supported by the identification of point mutations in α-Syn protein associated with rare familial forms of PD. However, the correlation between aggregation propensities of α-Syn mutants and their association with PD phenotype is not straightforward. Recent evidence suggested that oligomers, formed during the initial stages of aggregation, are the potent neurotoxic species causing cell death in PD. However, the heterogeneous and unstable nature of these oligomers limit their detailed characterization. α-Syn fibrils, on the contrary, are shown to be the infectious agents and propagate in a prion-like manner. Although α-Syn is an intrinsically disordered protein, it exhibits remarkable conformational plasticity by adopting a range of structural conformations under different environmental conditions. In this review, we focus on the structural and functional aspects of α-Syn and role of potential factors that may contribute to the underlying mechanism of synucleinopathies. This information will help to identify novel targets and develop specific therapeutic strategies to combat Parkinson's and other protein aggregation related neurodegenerative diseases.
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25
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Abstract
Protein oligomers are increasingly recognized as the most cytotoxic forms of protein aggregates. It has been very challenging, however, to target these oligomers with therapeutic compounds, because of their dynamic and transient nature. To overcome this problem, we present here a “structure–kinetic-activity relationship” (SKAR) approach, which enables the discovery and systematic optimization of compounds that reduce the number of oligomers produced during an aggregation reaction. We illustrate this strategy for the amyloid beta peptide (Aβ), which is closely associated with Alzheimer’s disease, by developing a rhodanine compound capable of dramatically reducing the production of Aβ oligomers. As this strategy is general, it can be applied to oligomers of any protein. To develop effective therapeutic strategies for protein misfolding diseases, a promising route is to identify compounds that inhibit the formation of protein oligomers. To achieve this goal, we report a structure−activity relationship (SAR) approach based on chemical kinetics to estimate quantitatively how small molecules modify the reactive flux toward oligomers. We use this estimate to derive chemical rules in the case of the amyloid beta peptide (Aβ), which we then exploit to optimize starting compounds to curtail Aβ oligomer formation. We demonstrate this approach by converting an inactive rhodanine compound into an effective inhibitor of Aβ oligomer formation by generating chemical derivatives in a systematic manner. These results provide an initial demonstration of the potential of drug discovery strategies based on targeting directly the production of protein oligomers.
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26
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Iashchishyn IA, Gruden MA, Moskalenko RA, Davydova TV, Wang C, Sewell RDE, Morozova-Roche LA. Intranasally Administered S100A9 Amyloids Induced Cellular Stress, Amyloid Seeding, and Behavioral Impairment in Aged Mice. ACS Chem Neurosci 2018; 9:1338-1348. [PMID: 29618200 DOI: 10.1021/acschemneuro.7b00512] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Amyloid formation and neuroinflammation are major features of Alzheimer's disease pathology. Proinflammatory mediator S100A9 was shown to act as a link between the amyloid and neuroinflammatory cascades in Alzheimer's disease, leading together with Aβ to plaque formation, neuronal loss and memory impairment. In order to examine if S100A9 alone in its native and amyloid states can induce neuronal stress and memory impairment, we have administered S100A9 species intranasally to aged mice. Single and sequential immunohistochemistry and passive avoidance behavioral test were conducted to evaluate the consequences. Administered S100A9 species induced widespread cellular stress responses in cerebral structures, including frontal lobe, hippocampus and cerebellum. These were manifested by increased levels of S100A9, Bax, and to a lesser extent activated caspase-3 immunopositive cells. Upon administration of S100A9 fibrils, the amyloid oligomerization was observed in the brain tissues, which can further exacerbate cellular stress. The cellular stress responses correlated with significantly increased training and decreased retention latencies measured in the passive avoidance test for the S100A9 treated animal groups. Remarkably, the effect size in the behavioral tests was moderate already in the group treated with native S100A9, while the effect sizes were large in the groups administered S100A9 amyloid oligomers or fibrils. The findings demonstrate the brain susceptibility to neurotoxic damage of S100A9 species leading to behavioral and memory impairments. Intranasal administration of S100A9 species proved to be an effective method to study amyloid induced brain dysfunctions, and S100A9 itself may be postulated as a target to allay early stage neurodegenerative and neuroinflammatory processes.
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Affiliation(s)
- Igor A. Iashchishyn
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-90187, Sweden
- Department of General Chemistry, Sumy State University, Sumy 40007, Ukraine
| | - Marina A. Gruden
- Department of Functional Neurochemistry, P. K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia
| | - Roman A. Moskalenko
- Department of Pathology, Sumy State University, Sumy 40007, Ukraine
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-90187, Sweden
| | - Tatiana V. Davydova
- Department of Neuroimmunopathology, Research Institute of General Pathology and Pathophysiology, Moscow 125315, Russia
| | - Chao Wang
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-90187, Sweden
| | - Robert D. E. Sewell
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, United Kingdom
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27
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Wright MA, Aprile FA, Bellaiche MMJ, Michaels TCT, Müller T, Arosio P, Vendruscolo M, Dobson CM, Knowles TPJ. Cooperative Assembly of Hsp70 Subdomain Clusters. Biochemistry 2018; 57:3641-3649. [PMID: 29763298 PMCID: PMC6202011 DOI: 10.1021/acs.biochem.8b00151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Many molecular chaperones exist as oligomeric complexes in their functional states, yet the physical determinants underlying such self-assembly behavior, as well as the role of oligomerization in the activity of molecular chaperones in inhibiting protein aggregation, have proven to be difficult to define. Here, we demonstrate direct measurements under native conditions of the changes in the average oligomer populations of a chaperone system as a function of concentration and time and thus determine the thermodynamic and kinetic parameters governing the self-assembly process. We access this self-assembly behavior in real time under native-like conditions by monitoring the changes in the micrometer-scale diffusion of the different complexes in time and space using a microfluidic platform. Using this approach, we find that the oligomerization mechanism of the Hsp70 subdomain occurs in a cooperative manner and involves structural constraints that limit the size of the species formed beyond the limits imposed by mass balance. These results illustrate the ability of microfluidic methods to probe polydisperse protein self-assembly in real time in solution and to shed light on the nature and dynamics of oligomerization processes.
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Affiliation(s)
- Maya A Wright
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Fluidic Analytics Ltd. , Cambridge , U.K
| | - Francesco A Aprile
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Mathias M J Bellaiche
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Thomas C T Michaels
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Thomas Müller
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Fluidic Analytics Ltd. , Cambridge , U.K
| | - Paolo Arosio
- Institute for Chemical and Bioengineering , ETH Zurich , Vladimir-Prelog-Weg 1, ETH Hönggerberg, HCI F 105 , 8093 Zurich , Switzerland
| | - Michele Vendruscolo
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Christopher M Dobson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Cavendish Laboratory, Department of Physics , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
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28
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Cholesterol catalyses Aβ42 aggregation through a heterogeneous nucleation pathway in the presence of lipid membranes. Nat Chem 2018; 10:673-683. [DOI: 10.1038/s41557-018-0031-x] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/20/2018] [Indexed: 02/03/2023]
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29
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Maury CPJ. Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities. Cell Mol Life Sci 2018; 75:1499-1507. [PMID: 29550973 PMCID: PMC5897472 DOI: 10.1007/s00018-018-2797-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/19/2018] [Accepted: 03/13/2018] [Indexed: 01/29/2023]
Abstract
A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.
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Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation. Annu Rev Phys Chem 2018; 69:273-298. [PMID: 29490200 DOI: 10.1146/annurev-physchem-050317-021322] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.
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Affiliation(s)
- Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, and Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 1HE, United Kingdom; ,
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31
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Carbonell F, Iturria-Medina Y, Evans AC. Mathematical Modeling of Protein Misfolding Mechanisms in Neurological Diseases: A Historical Overview. Front Neurol 2018; 9:37. [PMID: 29456521 PMCID: PMC5801313 DOI: 10.3389/fneur.2018.00037] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/16/2018] [Indexed: 12/12/2022] Open
Abstract
Protein misfolding refers to a process where proteins become structurally abnormal and lose their specific 3-dimensional spatial configuration. The histopathological presence of misfolded protein (MP) aggregates has been associated as the primary evidence of multiple neurological diseases, including Prion diseases, Alzheimer's disease, Parkinson's disease, and Creutzfeldt-Jacob disease. However, the exact mechanisms of MP aggregation and propagation, as well as their impact in the long-term patient's clinical condition are still not well understood. With this aim, a variety of mathematical models has been proposed for a better insight into the kinetic rate laws that govern the microscopic processes of protein aggregation. Complementary, another class of large-scale models rely on modern molecular imaging techniques for describing the phenomenological effects of MP propagation over the whole brain. Unfortunately, those neuroimaging-based studies do not take full advantage of the tremendous capabilities offered by the chemical kinetics modeling approach. Actually, it has been barely acknowledged that the vast majority of large-scale models have foundations on previous mathematical approaches that describe the chemical kinetics of protein replication and propagation. The purpose of the current manuscript is to present a historical review about the development of mathematical models for describing both microscopic processes that occur during the MP aggregation and large-scale events that characterize the progression of neurodegenerative MP-mediated diseases.
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Affiliation(s)
| | - Yasser Iturria-Medina
- Department of Neurology & Neurosurgery, McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, QC, Canada
- Ludmer Centre for NeuroInformatics and Mental Health, Montreal, QC, Canada
| | - Alan C. Evans
- Department of Neurology & Neurosurgery, McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, QC, Canada
- Ludmer Centre for NeuroInformatics and Mental Health, Montreal, QC, Canada
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32
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Zamorano Cuervo N, Osseman Q, Grandvaux N. Virus Infection Triggers MAVS Polymers of Distinct Molecular Weight. Viruses 2018; 10:E56. [PMID: 29385716 PMCID: PMC5850363 DOI: 10.3390/v10020056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/24/2018] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
The mitochondrial antiviral signaling (MAVS) adaptor protein is a central signaling hub required for cells to mount an antiviral response following virus sensing by retinoic acid-inducible gene I (RIG-I)-like receptors. MAVS localizes in the membrane of mitochondria and peroxisomes and in mitochondrial-associated endoplasmic reticulum membranes. Structural and functional studies have revealed that MAVS activity relies on the formation of functional high molecular weight prion-like aggregates. The formation of protein aggregates typically relies on a dynamic transition between oligomerization and aggregation states. The existence of intermediate state(s) of MAVS polymers, other than aggregates, has not yet been documented. Here, we used a combination of non-reducing SDS-PAGE and semi-denaturing detergent agarose gel electrophoresis (SDD-AGE) to resolve whole cell extract preparations to distinguish MAVS polymerization states. While SDD-AGE analysis of whole cell extracts revealed the formation of previously described high molecular weight prion-like aggregates upon constitutively active RIG-I ectopic expression and virus infection, non-reducing SDS-PAGE allowed us to demonstrate the induction of lower molecular weight oligomers. Cleavage of MAVS using the NS3/4A protease revealed that anchoring to intracellular membranes is required for the appropriate polymerization into active high molecular weight aggregates. Altogether, our data suggest that RIG-I-dependent MAVS activation involves the coexistence of MAVS polymers with distinct molecular weights.
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Affiliation(s)
- Natalia Zamorano Cuervo
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada.
| | - Quentin Osseman
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada.
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
| | - Nathalie Grandvaux
- CRCHUM-Centre Hospitalier de l'Université de Montréal, 900 rue Saint Denis, Montréal, QC H2X 0A9, Canada.
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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33
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Ruggeri FS, Habchi J, Cerreta A, Dietler G. AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species. Curr Pharm Des 2017; 22:3950-70. [PMID: 27189600 PMCID: PMC5080865 DOI: 10.2174/1381612822666160518141911] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/17/2016] [Indexed: 01/05/2023]
Abstract
Background A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established. Methods: In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species. Conclusion: The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases.
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Affiliation(s)
- Francesco Simone Ruggeri
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom.
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34
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Branch T, Barahona M, Dodson CA, Ying L. Kinetic Analysis Reveals the Identity of Aβ-Metal Complex Responsible for the Initial Aggregation of Aβ in the Synapse. ACS Chem Neurosci 2017. [PMID: 28621929 PMCID: PMC5609119 DOI: 10.1021/acschemneuro.7b00121] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
![]()
The
mechanism of Aβ aggregation in the absence of metal ions
is well established, yet the role that Zn2+ and Cu2+, the two most studied metal ions, released during neurotransmission,
paly in promoting Aβ aggregation in the vicinity of neuronal
synapses remains elusive. Here we report the kinetics of Zn2+ binding to Aβ and Zn2+/Cu2+ binding
to Aβ-Cu to form ternary complexes under near physiological
conditions (nM Aβ, μM metal ions). We find that these
reactions are several orders of magnitude slower than Cu2+ binding to Aβ. Coupled reaction-diffusion simulations of the
interactions of synaptically released metal ions with Aβ show
that up to a third of Aβ is Cu2+-bound under repetitive
metal ion release, while any other Aβ-metal complexes (including
Aβ-Zn) are insignificant. We therefore conclude that Zn2+ is unlikely to play an important role in the very early
stages (i.e., dimer formation) of Aβ aggregation, contrary to
a widely held view in the subject. We propose that targeting the specific
interactions between Cu2+ and Aβ may be a viable
option in drug development efforts for early stages of AD.
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Affiliation(s)
- Thomas Branch
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mauricio Barahona
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Charlotte A. Dodson
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
| | - Liming Ying
- Institute of Chemical Biology, ‡Department of Chemistry, §Department of Mathematics, and ∥National Heart
and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
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35
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Wei G, Su Z, Reynolds NP, Arosio P, Hamley IW, Gazit E, Mezzenga R. Self-assembling peptide and protein amyloids: from structure to tailored function in nanotechnology. Chem Soc Rev 2017; 46:4661-4708. [PMID: 28530745 PMCID: PMC6364806 DOI: 10.1039/c6cs00542j] [Citation(s) in RCA: 538] [Impact Index Per Article: 76.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Self-assembled peptide and protein amyloid nanostructures have traditionally been considered only as pathological aggregates implicated in human neurodegenerative diseases. In more recent times, these nanostructures have found interesting applications as advanced materials in biomedicine, tissue engineering, renewable energy, environmental science, nanotechnology and material science, to name only a few fields. In all these applications, the final function depends on: (i) the specific mechanisms of protein aggregation, (ii) the hierarchical structure of the protein and peptide amyloids from the atomistic to mesoscopic length scales and (iii) the physical properties of the amyloids in the context of their surrounding environment (biological or artificial). In this review, we will discuss recent progress made in the field of functional and artificial amyloids and highlight connections between protein/peptide folding, unfolding and aggregation mechanisms, with the resulting amyloid structure and functionality. We also highlight current advances in the design and synthesis of amyloid-based biological and functional materials and identify new potential fields in which amyloid-based structures promise new breakthroughs.
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Affiliation(s)
- Gang Wei
- Faculty of Production Engineering, University of Bremen, Bremen,
Germany
| | - Zhiqiang Su
- State Key Laboratory of Chemical Resource Engineering, Beijing
University of Chemical Technology, China
| | - Nicholas P. Reynolds
- ARC Training Centre for Biodevices, Swinburne University of
Technology, Melbourne, Australia
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH-Zurich,
Switzerland
| | | | - Ehud Gazit
- Faculty of Life Sciences, Tel Aviv University, Israel
| | - Raffaele Mezzenga
- Department of Health Science and Technology, ETH-Zurich,
Switzerland
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36
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Akter R, Abedini A, Ridgway Z, Zhang X, Kleinberg J, Schmidt AM, Raleigh DP. Evolutionary Adaptation and Amyloid Formation: Does the Reduced Amyloidogenicity and Cytotoxicity of Ursine Amylin Contribute to the Metabolic Adaption of Bears and Polar Bears? Isr J Chem 2017; 57:750-761. [PMID: 29955200 PMCID: PMC6018008 DOI: 10.1002/ijch.201600081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Much of our knowledge of diabetes is derived from studies of rodent models. An alternative approach explores evolutionary solutions to physiological stress by studying organisms that face challenging metabolic environments. Polar bears eat an enormously lipid-rich diet without deleterious metabolic consequences. In contrast, transgenic rodents expressing the human neuropancreatic polypeptide hormone amylin develop hyperglycemia and extensive pancreatic islet amyloid when fed a high fat diet. The process of islet amyloid formation by human amylin contributes to β-cell dysfunction and loss of β-cell mass in type-2 diabetes. We show that ursine amylin is considerably less amyloidogenic and less toxic to β-cells than human amylin, consistent with the hypothesis that part of the adaptation of bears to metabolic challenges might include protection from islet amyloidosis-induced β-cell toxicity. Ursine and human amylin differ at four locations: H18R, S20G, F23L, and S29P. These are interesting from a biophysical perspective since the S20G mutation accelerates amyloid formation but the H18R slows it. An H18RS20G double mutant of human amylin behaves similarly to the H18R mutant, indicating that the substitution at position 18 dominates the S20G replacement. These data suggest one possible mechanism underpinning the protection of bears against metabolic challenges and provide insight into the design of soluble analogs of human amylin.
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Affiliation(s)
- Rehana Akter
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Andisheh Abedini
- Diabetes Research Program, NYU School of Medicine, 522 First Avenue, New York, NY 10016
| | - Zachary Ridgway
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Xiaoxue Zhang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Joel Kleinberg
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
| | - Ann Marie Schmidt
- Diabetes Research Program, NYU School of Medicine, 522 First Avenue, New York, NY 10016
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400
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37
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Michaels TCT, Liu LX, Meisl G, Knowles TPJ. Physical principles of filamentous protein self-assembly kinetics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:153002. [PMID: 28170349 DOI: 10.1088/1361-648x/aa5f10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer's and Parkinson's diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.
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Affiliation(s)
- Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, United States of America
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38
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Michel D, Ruelle P. Polylogarithmic equilibrium treatment of molecular aggregation and critical concentrations. Phys Chem Chem Phys 2017; 19:5273-5284. [DOI: 10.1039/c6cp08369b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new modeling approach to molecular aggregation is proposed under the condition of generalized microreversibility.
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Affiliation(s)
- Denis Michel
- Universite de Rennes1-IRSET
- Campus de Villejean
- 3500 Rennes
- France
| | - Philippe Ruelle
- Université catholique de Louvain – Institut de Recherche en Mathématique et Physique
- Chemin du Cyclotron
- 2 B-1348 Louvain-la-Neuve
- Belgium
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39
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Michaels TC, Dear AJ, Knowles TP. Scaling and dimensionality in the chemical kinetics of protein filament formation. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1239335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ, Frenkel D. Physical determinants of the self-replication of protein fibrils. NATURE PHYSICS 2016; 12:874-880. [PMID: 31031819 PMCID: PMC6485595 DOI: 10.1038/nphys3828] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/15/2016] [Indexed: 05/02/2023]
Abstract
The ability of biological molecules to replicate themselves, achieved with the aid of a complex cellular machinery, is the foundation of life. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional factors. A dramatic example is the autocatalytic replication of pathological protein aggregates, including amyloid fibrils and prions, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can only take place in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer's disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.
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Affiliation(s)
- Anđela Šarić
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | - Alexander K Buell
- Institute of Physical Biology, University of Duesseldorf, Duesseldorf Germany
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | | | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | | | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge, UK
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41
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Carballo-Pacheco M, Strodel B. Advances in the Simulation of Protein Aggregation at the Atomistic Scale. J Phys Chem B 2016; 120:2991-9. [PMID: 26965454 DOI: 10.1021/acs.jpcb.6b00059] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein aggregation into highly structured amyloid fibrils is associated with various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also have normal biological functions and, in the future, could be used as the basis for novel nanoscale materials. However, a full understanding of the physicochemical forces that drive protein aggregation is still lacking. Such understanding is crucial for the development of drugs that can effectively inhibit aberrant amyloid aggregation and for the directed design of functional amyloids. Atomistic simulations can help understand protein aggregation. In particular, atomistic simulations can be used to study the initial formation of toxic oligomers which are hard to characterize experimentally and to understand the difference in aggregation behavior between different amyloidogenic peptides. Here, we review the latest atomistic simulations of protein aggregation, concentrating on amyloidogenic protein fragments, and provide an outlook for the future in this field.
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Affiliation(s)
- Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich, 52425 Jülich, Germany.,AICES Graduate School, RWTH Aachen University , Schinkelstraße 2, 52062 Aachen, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich, 52425 Jülich, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, 40225 Düsseldorf, Germany
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