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Mahato J, Mukherjee R, Bose A, Mehra S, Gadhe L, Maji SK, Chowdhury A. Sensitized Emission Imaging Allows Nanoscale Surface Polarity Mapping of α-Synuclein Amyloid Fibrils. ACS Chem Neurosci 2024; 15:108-118. [PMID: 38099928 DOI: 10.1021/acschemneuro.3c00467] [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: 01/04/2024] Open
Abstract
When misfolded, α-Synuclein (α-Syn), a natively disordered protein, aggregates to form amyloid fibrils responsible for the neurodegeneration observed in Parkinson's disease. Structural studies revealed distinct molecular packing of α-Syn in different fibril polymorphs and variations of interprotofilament connections in the fibrillar architecture. Fibril polymorphs have been hypothesized to exhibit diverse surface polarities depending on the folding state of the protein during aggregation; however, the spatial variation of surface polarity in amyloid fibrils remains unexplored. To map the local polarity (or hydrophobicity) along α-Syn fibrils, we visualized the spectral characteristics of two dyes with distinct polarities-hydrophilic Thioflavin T (ThT) and hydrophobic Nile red (NR)─when both are bound to α-Syn fibrils. Dual-channel fluorescence imaging reveals uneven partitioning of ThT and NR along individual fibrils, implying that relatively more polar/hydrophobic patches are spread over a few hundred nanometers. Remarkably, spectrally resolved sensitized emission imaging of α-Syn fibrils provides unambiguous evidence of energy transfer from ThT to NR, implying that dyes of dissimilar polarity are in close proximity. Furthermore, spatially resolved fluorescence spectroscopy of the solvatochromic probe NR allowed us to quantitatively map the range and variation of the polarity parameter ET30 along individual fibrils. Our results suggest the existence of interlaced polar and nonpolar nanoscale domains throughout the fibrils; however, the relative populations of these patches vary considerably over larger length scales likely due to heterogeneous packing of α-Syn during fibrilization and dissimilar exposed polarities of polymorphic segments. The employed method may provide a foundation for imaging modalities of other similar structurally unresolved systems with diverse hydrophobic-hydrophilic topology.
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Affiliation(s)
- Jaladhar Mahato
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Rajat Mukherjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Abhik Bose
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
- Sunita Sanghi Centre of Ageing and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
- Sunita Sanghi Centre of Ageing and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai 400076, Mumbai, India
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2
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Tira R, Viola G, Barracchia CG, Parolini F, Munari F, Capaldi S, Assfalg M, D'Onofrio M. Espresso Coffee Mitigates the Aggregation and Condensation of Alzheimer's Associated Tau Protein. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37466260 PMCID: PMC10401709 DOI: 10.1021/acs.jafc.3c01072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Espresso coffee is among the most consumed beverages in the world. Recent studies report a protective activity of the coffee beverage against neurodegenerative disorders such as Alzheimer's disease. Alzheimer's disease belongs to a group of disorders, called tauopathies, which are characterized by the intraneuronal accumulation of the microtubule-associated protein tau in fibrillar aggregates. In this work, we characterized by NMR the molecular composition of the espresso coffee extract and identified its main components. We then demonstrated with in vitro and in cell experiments that the whole coffee extract, caffeine, and genistein have biological properties in preventing aggregation, condensation, and seeding activity of the repeat region of tau. We also identified a set of coffee compounds capable of binding to preformed tau fibrils. These results add insights into the neuroprotective potential of espresso coffee and suggest candidate molecular scaffolds for designing therapies targeting monomeric or fibrillized forms of tau.
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Affiliation(s)
- Roberto Tira
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 34134 Verona, Italy
| | - Giovanna Viola
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 34134 Verona, Italy
| | | | - Francesca Parolini
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 34134 Verona, Italy
| | - Francesca Munari
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 34134 Verona, Italy
| | - Stefano Capaldi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 34134 Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 34134 Verona, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 34134 Verona, Italy
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3
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Devi S, Chaturvedi M, Fatima S, Priya S. Environmental factors modulating protein conformations and their role in protein aggregation diseases. Toxicology 2022; 465:153049. [PMID: 34818560 DOI: 10.1016/j.tox.2021.153049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/12/2021] [Accepted: 11/20/2021] [Indexed: 12/13/2022]
Abstract
The adverse physiological conditions have been long known to impact protein synthesis, folding and functionality. Major physiological factors such as the effect of pH, temperature, salt and pressure are extensively studied for their impact on protein structure and homeostasis. However, in the current scenario, the environmental risk factors (pollutants) have gained impetus in research because of their increasing concentrations in the environment and strong epidemiologic link with protein aggregation disorders. Here, we review the physiological and environmental risk factors for their impact on protein conformational changes, misfolding, aggregation, and associated pathological conditions, especially environmental risk factors associated pathologies.
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Affiliation(s)
- Shweta Devi
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Minal Chaturvedi
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Siraj Fatima
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Smriti Priya
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Mahato J, Ray KK, Das S, Kadu P, Maji SK, Chowdhury A. Investigation of Structural Heterogeneity in Individual Amyloid Fibrils Using Polarization-Resolved Microscopy. J Phys Chem B 2021; 125:13406-13414. [PMID: 34861110 DOI: 10.1021/acs.jpcb.1c08604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid fibrils are structurally heterogeneous protein aggregates that are implicated in a wide range of neurodegenerative and other proteopathic diseases. These fibrils exist in a variety of different tertiary and higher-level structures, and this exhibited polymorphism greatly complicates any structural study of amyloid fibrils. In this work, we demonstrate a method of using polarization-resolved microscopy to directly observe the structural heterogeneity of individual amyloid fibrils using amyloid-bound fluorophores. We formulate a mathematical quantity, helical anisotropy, which utilizes the polarized emission of amyloid-bound fluorophores to report on the local structure of individual fibrils. Using this method, we show how model amyloid fibrils generated from short peptides exhibit diverse structural properties both between different fibrils and within a single fibril, in a manner that is replicated for fibrils assembled from longer proteins. Our method represents an accessible and easily adaptable technique by which polymorphism in the structure of amyloid fibrils can be probed. Additionally, the methodology we describe here can be easily extended to the study of other fibrillar and otherwise ordered supramolecular structures.
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Affiliation(s)
- Jaladhar Mahato
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Korak Kumar Ray
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Subhadeep Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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5
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Toward the equilibrium and kinetics of amyloid peptide self-assembly. Curr Opin Struct Biol 2021; 70:87-98. [PMID: 34153659 DOI: 10.1016/j.sbi.2021.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/09/2021] [Accepted: 05/09/2021] [Indexed: 01/28/2023]
Abstract
Several devastating human diseases are linked to peptide self-assembly, but our understanding their onset and progression is not settled. This is a sign of the complexity of the aggregation process, which is prevented, catalyzed, or retarded by numerous factors in body fluids and cells, varying in time and space. Biophysical studies of pure peptide solutions contribute insights into the underlying steps in the process and quantitative parameters relating to rate constants (energy barriers) and equilibrium constants (population distributions). This requires methods to quantify the concentration of at least one species in the process. Translation to an in vivo situation poses an enormous challenge, and the effects of selected components (bottom up) or entire body fluids (top down) need to be quantified.
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6
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Zhu L, Xu L, Wu X, Deng F, Ma R, Liu Y, Huang F, Shi L. Tau-Targeted Multifunctional Nanoinhibitor for Alzheimer's Disease. ACS APPLIED MATERIALS & INTERFACES 2021; 13:23328-23338. [PMID: 33999598 DOI: 10.1021/acsami.1c00257] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the failure of various amyloid-β-targeted drugs for Alzheimer's disease (AD) in clinical trials, tau protein has gained growing attention as an alternative therapeutic target in recent years. The aggregation of tau exerts neurotoxicity, and its spreading in the brain is associated with increasing severity of clinical symptoms for AD patients; thus tau-targeting therapies hold great potential against AD. Here, a tau-targeted multifunctional nanoinhibitor based on self-assembled polymeric micelles decorated with tau-binding peptide is devised for AD treatment. Through the multivalent binding effect with the aggregating protein, this nanoinhibitor is capable of efficiently inhibiting tau protein aggregation, recognizing tau aggregates, and blocking their seeding in neural cells, thus remarkably mitigating tau-mediated cytotoxicity. Moreover, the formed nanoinhibitor-tau complex after binding is more easily degraded than mature tau aggregates, which will be conducive to enhance the therapeutic effect. We believe that this multifunctional nanoinhibitor will promote the development of new antitau strategies for AD treatment.
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Affiliation(s)
- Lin Zhu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Linlin Xu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xiaohui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Fei Deng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Rujiang Ma
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Fan Huang
- Key Laboratory of Radiopharmacokinetics for Innovative Drugs, Chinese Academy of Medical Sciences, and Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, P. R. China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Functional Polymer Materials of Ministry of Education, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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7
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Ghaeidamini M, Bernson D, Sasanian N, Kumar R, Esbjörner EK. Graphene oxide sheets and quantum dots inhibit α-synuclein amyloid formation by different mechanisms. NANOSCALE 2020; 12:19450-19460. [PMID: 32959853 DOI: 10.1039/d0nr05003b] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aggregation and amyloid formation of the 140-residue presynaptic and intrinsically disordered protein α-synuclein (α-syn) is a pathological hallmark of Parkinson's disease (PD). Understanding how α-syn forms amyloid fibrils, and investigations of agents that can prevent their formation is therefore important. We demonstrate herein that two types of graphene oxide nanoparticles (sheets and quantum dots) inhibit α-syn amyloid formation by different mechanisms mediated via differential interactions with both monomers and fibrils. We have used thioflavin-T fluorescence assays and kinetic analysis, circular dichroism, dynamic light scattering, fluorescence spectroscopy and atomic force microscopy to asses the kinetic nature and efficiency of this inhibitory effect. We show that the two types of graphene oxide nanoparticles alter the morphology of α-syn fibrils, disrupting their interfilament assembly and the resulting aggregates therefore consist of single protofilaments. Our results further show that graphene oxide sheets reduce the aggregation rate of α-syn primarily by sequestering of monomers, thereby preventing primary nucleation and elongation. Graphene quantum dots, on the other hand, interact less avidly with both monomers and fibrils. Their aggregation inhibitory effect is primarily related to adsorption of aggregated species and reduction of secondary processes, and they can thus not fully prevent aggregation. This fine-tuned and differential effect of graphene nanoparticles on amyloid formation shows that rational design of these nanomaterials has great potential in engineering materials that interact with specific molecular events in the amyloid fibril formation process. The findings also provide new insight into the molecular interplay between amyloidogenic proteins and graphene-based nanomaterials in general, and opens up their potential use as agents to manipulate fibril formation.
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Affiliation(s)
- Marziyeh Ghaeidamini
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden.
| | - David Bernson
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden.
| | - Nima Sasanian
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden.
| | - Ranjeet Kumar
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden.
| | - Elin K Esbjörner
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, S-412 96 Gothenburg, Sweden.
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8
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Zhang Y, Ren B, Zhang D, Liu Y, Zhang M, Zhao C, Zheng J. Design principles and fundamental understanding of biosensors for amyloid-β detection. J Mater Chem B 2020; 8:6179-6196. [DOI: 10.1039/d0tb00344a] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aβ as biomarker in Alzheimer’s disease (AD) drives the significant research efforts for developing different biosensors with different sensing strategies, materials, and mechanisms for Aβ detection.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Baiping Ren
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Dong Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Yonglan Liu
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Mingzhen Zhang
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
| | - Chao Zhao
- Department of Chemical and Biomolecular Engineering
- The University of Alabama
- USA
| | - Jie Zheng
- Department of Chemical
- Biomolecular, and Corrosion Engineering
- The University of Akron
- Ohio
- USA
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9
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Aviolat H, Nominé Y, Gioria S, Bonhoure A, Hoffmann D, Ruhlmann C, Nierengarten H, Ruffenach F, Villa P, Trottier Y, Klein FAC. SynAggreg: A Multifunctional High-Throughput Technology for Precision Study of Amyloid Aggregation and Systematic Discovery of Synergistic Inhibitor Compounds. J Mol Biol 2018; 430:5257-5279. [PMID: 30266595 DOI: 10.1016/j.jmb.2018.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/30/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022]
Abstract
Numerous proteins can coalesce into amyloid self-assemblies, which are responsible for a class of diseases called amyloidoses, but which can also fulfill important biological functions and are of great interest for biotechnology. Amyloid aggregation is a complex multi-step process, poorly prone to detailed structural studies. Therefore, small molecules interacting with amyloids are often used as tools to probe the amyloid aggregation pathway and in some cases to treat amyloidoses as they prevent pathogenic protein aggregation. Here, we report on SynAggreg, an in vitro high-throughput (HT) platform dedicated to the precision study of amyloid aggregation and the effect of modulator compounds. SynAggreg relies on an accurate bi-fluorescent amyloid-tracer readout that overcomes some limitations of existing HT methods. It allows addressing diverse aspects of aggregation modulation that are critical for pathomechanistic studies, such as the specificity of compounds toward various amyloids and their effects on aggregation kinetics, as well as the co-assembly propensity of distinct amyloids and the influence of prion-like seeding on self-assembly. Furthermore, SynAggreg is the first HT technology that integrates tailored methodology to systematically identify synergistic compound combinations-an emerging strategy to improve fatal amyloidoses by targeting multiple steps of the aggregation pathway. To this end, we apply analytical combinatorial scores to rank the inhibition efficiency of couples of compounds and to readily detect synergism. Finally, the SynAggreg platform should be suited for the characterization of a broad class of amyloids, whether of interest for drug development purposes, for fundamental research on amyloid functions, or for biotechnological applications.
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Affiliation(s)
- Hubert Aviolat
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France
| | - Yves Nominé
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France
| | - Sophie Gioria
- University of Strasbourg, Strasbourg, France; Integrative Biological Chemistry Platform of Strasbourg, Illkirch, France
| | - Anna Bonhoure
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France
| | - David Hoffmann
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France
| | - Christine Ruhlmann
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France
| | - Hélène Nierengarten
- University of Strasbourg, Strasbourg, France; Institut de Chimie de Strasbourg, UMR7177, Strasbourg, France
| | - Frank Ruffenach
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France
| | - Pascal Villa
- University of Strasbourg, Strasbourg, France; Integrative Biological Chemistry Platform of Strasbourg, Illkirch, France; Centre National de la Recherche Scientifique, UMS 3286, Illkirch, France
| | - Yvon Trottier
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France.
| | - Fabrice A C Klein
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; University of Strasbourg, Strasbourg, France.
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Quinolinic Acid Amyloid-like Fibrillar Assemblies Seed α-Synuclein Aggregation. J Mol Biol 2018; 430:3847-3862. [PMID: 30098337 DOI: 10.1016/j.jmb.2018.08.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/17/2018] [Accepted: 08/01/2018] [Indexed: 01/08/2023]
Abstract
Quinolinic acid (QA), a downstream neurometabolite in the kynurenine pathway, the biosynthetic pathway of tryptophan, is associated with neurodegenerative diseases pathology. Mutations in genes encoding kynurenine pathway enzymes, which control the level of QA production, are linked with elevated risk of developing Parkinson's disease. Recent findings have revealed the accumulation and deposition of QA in post-mortem samples, as well as in cellular models of Alzheimer's disease and related disorders. Furthermore, intrastriatal inoculation of mice with QA results in increased levels of phosphorylated α-synuclein and neurodegenerative pathological and behavioral characteristics. However, the cellular and molecular mechanisms underlying the involvement of QA accumulation in protein aggregation and neurodegeneration remain elusive. We recently established that self-assembled ordered structures are formed by various metabolites and hypothesized that these "metabolite amyloids" may seed amyloidogenic proteins. Here we demonstrate the formation of QA amyloid-like fibrillar assemblies and seeding of α-synuclein aggregation by these nanostructures both in vitro and in cell culture. Notably, α-synuclein aggregation kinetics was accelerated by an order of magnitude. Additional amyloid-like properties of QA assemblies were demonstrated using thioflavin T assay, powder X-ray diffraction and cell apoptosis analysis. Moreover, fluorescently labeled QA assemblies were internalized by neuronal cells and co-localized with α-synuclein aggregates. In addition, we observed cell-to-cell propagation of fluorescently labeled QA assemblies in a co-culture of treated and untreated cells. Our findings suggest that excess QA levels, due to mutations in the kynurenine pathway, for example, may lead to the formation of metabolite assemblies that seed α-synuclein aggregation, resulting in neuronal toxicity and induction of Parkinson's disease.
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11
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Ribarič S. Peptides as Potential Therapeutics for Alzheimer's Disease. Molecules 2018; 23:E283. [PMID: 29385735 PMCID: PMC6017258 DOI: 10.3390/molecules23020283] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/22/2022] Open
Abstract
Intracellular synthesis, folding, trafficking and degradation of proteins are controlled and integrated by proteostasis. The frequency of protein misfolding disorders in the human population, e.g., in Alzheimer's disease (AD), is increasing due to the aging population. AD treatment options are limited to symptomatic interventions that at best slow-down disease progression. The key biochemical change in AD is the excessive accumulation of per-se non-toxic and soluble amyloid peptides (Aβ(1-37/44), in the intracellular and extracellular space, that alters proteostasis and triggers Aβ modification (e.g., by reactive oxygen species (ROS)) into toxic intermediate, misfolded soluble Aβ peptides, Aβ dimers and Aβ oligomers. The toxic intermediate Aβ products aggregate into progressively less toxic and less soluble protofibrils, fibrils and senile plaques. This review focuses on peptides that inhibit toxic Aβ oligomerization, Aβ aggregation into fibrils, or stabilize Aβ peptides in non-toxic oligomers, and discusses their potential for AD treatment.
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Affiliation(s)
- Samo Ribarič
- Institute of Pathophysiology, Faculty of Medicine, Zaloška 4, SI-1000 Ljubljana, Slovenia.
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12
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Shaham-Niv S, Rehak P, Zaguri D, Kolusheva S, Král P, Gazit E. Metabolite amyloid-like fibrils interact with model membranes. Chem Commun (Camb) 2018; 54:4561-4564. [DOI: 10.1039/c8cc01423j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metabolite assemblies interaction with membranes further extend the “amyloid hypothesis” to include small metabolites which serve as amyloidogenic building blocks.
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Affiliation(s)
- Shira Shaham-Niv
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 6997801
- Israel
| | - Pavel Rehak
- Department of Chemistry
- University of Illinois at Chicago
- Chicago
- USA
| | - Dor Zaguri
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 6997801
- Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology
- Ben Gurion University of the Negev
- Beer Sheva 84105
- Israel
| | - Petr Král
- Department of Chemistry
- University of Illinois at Chicago
- Chicago
- USA
- Department of Physics
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology
- George S. Wise Faculty of Life Sciences
- Tel Aviv University
- Tel Aviv 6997801
- Israel
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13
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Fisher E, Zhao Y, Richardson R, Janik M, Buell AK, Aigbirhio FI, Tóth G. Detection and Characterization of Small Molecule Interactions with Fibrillar Protein Aggregates Using Microscale Thermophoresis. ACS Chem Neurosci 2017. [PMID: 28640595 DOI: 10.1021/acschemneuro.7b00228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Neurodegenerative diseases such as Parkinson's and Alzheimer's disease share the pathological hallmark of fibrillar protein aggregates. The specific detection of these protein aggregates by positron emission tomography (PET) in the patient brain can yield valuable information for diagnosis and disease progression. However, the identification of novel small compounds that bind fibrillar protein aggregates has been a challenge. In this study, microscale thermophoresis (MST) was applied to assess the binding affinity of known small molecule ligands of α-synuclein fibrils, which were also tested in parallel in a thioflavin T fluorescence competition assay for further validation. In addition, a MST assay was also developed for the detection of the interaction between a variety of small molecules and tau fibrils. The results of this study demonstrate that MST is a powerful and practical methodology to quantify interactions between small molecules and protein fibrillar aggregates, which suggests that it can be applied for the identification and development of PET radioligands and potentially of therapeutic candidates for protein misfolding diseases.
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Affiliation(s)
- Emily Fisher
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Yanyan Zhao
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Robert Richardson
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Malgorzata Janik
- MTA-TTK-NAP
B, Drug Discovery Research Group, Neurodegenerative Diseases, Institute
of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1051, Hungary
| | - Alexander K. Buell
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Franklin I. Aigbirhio
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
| | - Gergely Tóth
- Molecular Imaging
Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of
Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, U.K
- MTA-TTK-NAP
B, Drug Discovery Research Group, Neurodegenerative Diseases, Institute
of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1051, Hungary
- Cantabio Pharmaceuticals Inc., Sunnyvale, California 94085, United States
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14
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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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15
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Lindberg DJ, Wenger A, Sundin E, Wesén E, Westerlund F, Esbjörner EK. Binding of Thioflavin-T to Amyloid Fibrils Leads to Fluorescence Self-Quenching and Fibril Compaction. Biochemistry 2017; 56:2170-2174. [DOI: 10.1021/acs.biochem.7b00035] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David J. Lindberg
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Anna Wenger
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Elin Sundin
- Division
of Chemistry and Biochemistry, Department of Chemistry and Chemical
Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Emelie Wesén
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Fredrik Westerlund
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Elin K. Esbjörner
- Division
of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
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16
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Nabuurs RJ, Kapoerchan VV, Metaxas A, Hafith S, de Backer M, Welling MM, Jiskoot W, van den Nieuwendijk AM, Windhorst AD, Overkleeft HS, van Buchem MA, Overhand M, van der Weerd L. Bis-pyridylethenyl benzene as novel backbone for amyloid-β binding compounds. Bioorg Med Chem 2016; 24:6139-6148. [PMID: 27838168 DOI: 10.1016/j.bmc.2016.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 04/28/2016] [Accepted: 05/14/2016] [Indexed: 11/16/2022]
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17
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Shaham-Niv S, Rehak P, Vuković L, Adler-Abramovich L, Král P, Gazit E. Formation of Apoptosis-Inducing Amyloid Fibrils by Tryptophan. Isr J Chem 2016. [DOI: 10.1002/ijch.201600076] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Shira Shaham-Niv
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv 69978 Israel
| | - Pavel Rehak
- Department of Chemistry; University of Illinois at Chicago; Chicago USA
| | - Lela Vuković
- Department of Chemistry; University of Texas at El Paso; El Paso USA
| | - Lihi Adler-Abramovich
- Department of Oral Biology; The Goldschleger School of Dental Medicine; Tel Aviv University; Tel Aviv 69978 Israel
| | - Petr Král
- Department of Chemistry; University of Illinois at Chicago; Chicago USA
- Department of Physics; University of Illinois at Chicago; Chicago USA
- Department of Biopharmaceutical Sciences; University of Illinois at Chicago; Chicago USA
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv 69978 Israel
- Department of Materials Science and Engineering; Iby and Aladar Fleischman Faculty of Engineering; Tel Aviv University; Tel Aviv 69978 Israel
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18
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Zhang Y, Buell AK, Müller T, De Genst E, Benesch J, Dobson CM, Knowles TPJ. Protein Aggregate-Ligand Binding Assays Based on Microfluidic Diffusional Separation. Chembiochem 2016; 17:1920-1924. [DOI: 10.1002/cbic.201600384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Yingbo Zhang
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Alexander K. Buell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Institute of Physical Biology; University of Düsseldorf; Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Thomas Müller
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Fluidic Analytics Ltd; Unit 5 Chesterton Mill; French's Road Cambridge CB4 3NP UK
| | - Erwin De Genst
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- AstraZeneca; Innovative Medicines, Discovery Sciences; Cambridge Science Park Milton Road Cambridge CB4 0WG UK
| | - Justin Benesch
- Department of Chemistry; Physical and Theoretical Chemistry Laboratory; University of Oxford; South Parks Road Oxford OX3 1QZ UK
| | - Christopher M. Dobson
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tuomas P. J. Knowles
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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19
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Lindberg DJ, Esbjörner EK. Detection of amyloid-β fibrils using the DNA-intercalating dye YOYO-1: Binding mode and fibril formation kinetics. Biochem Biophys Res Commun 2016; 469:313-8. [DOI: 10.1016/j.bbrc.2015.11.051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/11/2015] [Indexed: 11/30/2022]
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20
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Caillon L, Hoffmann ARF, Botz A, Khemtemourian L. Molecular Structure, Membrane Interactions, and Toxicity of the Islet Amyloid Polypeptide in Type 2 Diabetes Mellitus. J Diabetes Res 2016; 2016:5639875. [PMID: 26636105 PMCID: PMC4655289 DOI: 10.1155/2016/5639875] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/03/2015] [Indexed: 12/04/2022] Open
Abstract
Human islet amyloid polypeptide (hIAPP) is the major component of the amyloid deposits found in the pancreatic islets of patients with type 2 diabetes mellitus (T2DM). Mature hIAPP, a 37-aa peptide, is natively unfolded in its monomeric state but forms islet amyloid in T2DM. In common with other misfolded and aggregated proteins, amyloid formation involves aggregation of monomers of hIAPP into oligomers, fibrils, and ultimately mature amyloid deposits. hIAPP is coproduced and stored with insulin by the pancreatic islet β-cells and is released in response to the stimuli that lead to insulin secretion. Accumulating evidence suggests that hIAPP amyloid deposits that accompany T2DM are not just an insignificant phenomenon derived from the disease progression but that hIAPP aggregation induces processes that impair the functionality and the viability of β-cells. In this review, we particularly focus on hIAPP structure, hIAPP aggregation, and hIAPP-membrane interactions. We will also discuss recent findings on the mechanism of hIAPP-membrane damage and on hIAPP-induced cell death. Finally, the development of successful antiamyloidogenic agents that prevent hIAPP fibril formation will be examined.
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Affiliation(s)
- Lucie Caillon
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire des Biomolécules, 4 Place Jussieu, 75005 Paris, France
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, 24 Rue Lhomond, 75005 Paris, France
- CNRS, UMR 7203 Laboratoire des Biomolécules, 75005 Paris, France
| | - Anais R. F. Hoffmann
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire des Biomolécules, 4 Place Jussieu, 75005 Paris, France
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, 24 Rue Lhomond, 75005 Paris, France
- CNRS, UMR 7203 Laboratoire des Biomolécules, 75005 Paris, France
| | - Alexandra Botz
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire des Biomolécules, 4 Place Jussieu, 75005 Paris, France
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, 24 Rue Lhomond, 75005 Paris, France
- CNRS, UMR 7203 Laboratoire des Biomolécules, 75005 Paris, France
| | - Lucie Khemtemourian
- Sorbonne Universités, UPMC Univ Paris 06, Laboratoire des Biomolécules, 4 Place Jussieu, 75005 Paris, France
- Département de Chimie, Ecole Normale Supérieure, PSL Research University, 24 Rue Lhomond, 75005 Paris, France
- CNRS, UMR 7203 Laboratoire des Biomolécules, 75005 Paris, France
- *Lucie Khemtemourian:
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21
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Smith JE, Mowles AK, Mehta AK, Lynn DG. Looked at life from both sides now. Life (Basel) 2014; 4:887-902. [PMID: 25513758 PMCID: PMC4284472 DOI: 10.3390/life4040887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/25/2023] Open
Abstract
As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.
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Affiliation(s)
- Jillian E Smith
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Allisandra K Mowles
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - Anil K Mehta
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
| | - David G Lynn
- Department of Chemistry and Biology, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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22
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The physical chemistry of the amyloid phenomenon: thermodynamics and kinetics of filamentous protein aggregation. Essays Biochem 2014; 56:11-39. [DOI: 10.1042/bse0560011] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this chapter, we present an overview of the kinetics and thermodynamics of protein aggregation into amyloid fibrils. The perspective we adopt is largely experimental, but we also discuss recent developments in data analysis and we show that only a combination of well-designed experiments with appropriate theoretical modelling is able to provide detailed mechanistic insight into the complex pathways of amyloid formation. In the first part of the chapter, we describe measurements of the thermodynamic stability of the amyloid state with respect to the soluble state of proteins, as well as the magnitude and origin of this stability. In the second part, we discuss in detail the kinetics of the individual molecular steps in the overall mechanism of the conversion of soluble protein into amyloid fibrils. Finally, we highlight the effects of external factors, such as salt type and concentration, chemical denaturants and molecular chaperones on the kinetics of aggregation.
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23
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Huang F, Wang J, Qu A, Shen L, Liu J, Liu J, Zhang Z, An Y, Shi L. Maintenance of Amyloid β Peptide Homeostasis by Artificial Chaperones Based on Mixed-Shell Polymeric Micelles. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400735] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Huang F, Wang J, Qu A, Shen L, Liu J, Liu J, Zhang Z, An Y, Shi L. Maintenance of Amyloid β Peptide Homeostasis by Artificial Chaperones Based on Mixed-Shell Polymeric Micelles. Angew Chem Int Ed Engl 2014; 53:8985-90. [DOI: 10.1002/anie.201400735] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/20/2014] [Indexed: 01/14/2023]
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25
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Sjöqvist J, Linares M, Mikkelsen KV, Norman P. QM/MM-MD simulations of conjugated polyelectrolytes: a study of luminescent conjugated oligothiophenes for use as biophysical probes. J Phys Chem A 2014; 118:3419-28. [PMID: 24738472 DOI: 10.1021/jp5009835] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state as well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (iii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.
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Affiliation(s)
- Jonas Sjöqvist
- Department of Physics, Chemistry and Biology, Linköping University , SE-581 83 Linköping, Sweden
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26
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Nabuurs RJA, Kapoerchan VV, Metaxas A, de Jongh S, de Backer M, Welling MM, Jiskoot W, Windhorst AD, Overkleeft HS, van Buchem MA, Overhand M, van der Weerd L. Polyfluorinated bis-styrylbenzenes as amyloid-β plaque binding ligands. Bioorg Med Chem 2014; 22:2469-81. [PMID: 24657049 DOI: 10.1016/j.bmc.2014.02.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 02/25/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
Detection of cerebral β-amyloid (Aβ) by targeted contrast agents remains of great interest to aid the in vivo diagnosis of Alzheimer's disease (AD). Bis-styrylbenzenes have been previously reported as potential Aβ imaging agents. To further explore their potency as (19)F MRI contrast agents we synthetized several novel fluorinated bis-styrylbenzenes and studied their fluorescent properties and amyloid-β binding characteristics. The compounds showed a high affinity for Aβ plaques on murine and human brain sections. Interestingly, competitive binding experiments demonstrated that they bound to a different binding site than chrysamine G. Despite their high logP values, many bis-styrylbenzenes were able to enter the brain and label murine amyloid in vivo. Unfortunately initial post-mortem (19)F NMR studies showed that these compounds as yet do not warrant further MRI studies due to the reduction of the (19)F signal in the environment of the brain.
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Affiliation(s)
- Rob J A Nabuurs
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.
| | - Varsha V Kapoerchan
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | | | - Sanne de Jongh
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Maaike de Backer
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Mick M Welling
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Wim Jiskoot
- Division of Drug Delivery Technology, Leiden Academic Center for Drug Research, Leiden University, Netherlands
| | | | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Mark A van Buchem
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Mark Overhand
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Louise van der Weerd
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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27
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Arosio P, Vendruscolo M, Dobson CM, Knowles TPJ. Chemical kinetics for drug discovery to combat protein aggregation diseases. Trends Pharmacol Sci 2014; 35:127-35. [PMID: 24560688 DOI: 10.1016/j.tips.2013.12.005] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/17/2013] [Accepted: 12/12/2013] [Indexed: 12/24/2022]
Abstract
Protein misfolding diseases are becoming increasingly prevalent, yet there are very few effective pharmacological treatments. The onset and progression of these diseases is associated with the aberrant aggregation of normally soluble proteins and peptides into amyloid fibrils. Because genetic and physiological findings suggest that protein aggregation is a key event in pathogenesis, an attractive therapeutic strategy against this class of disorders is the search for compounds able to interfere with this process, in particular by suppressing the formation of soluble toxic oligomeric aggregates. In this review, we discuss how chemical kinetics can contribute to the fundamental understanding of the molecular mechanism of aggregation, and speculate on the implications for the development of therapeutic molecules that inhibit specific steps in the aggregation pathway that are crucial for preventing toxicity.
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Affiliation(s)
- Paolo Arosio
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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28
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Bleiholder C, Dupuis NF, Bowers MT. Dimerization of Chirally Mutated Enkephalin Neurotransmitters: Implications for Peptide and Protein Aggregation Mechanisms. J Phys Chem B 2013; 117:1770-9. [DOI: 10.1021/jp306386p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
93106, United States
| | - Nicholas F. Dupuis
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
93106, United States
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29
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Murugan NA, Olsen JMH, Kongsted J, Rinkevicius Z, Aidas K, Ågren H. Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe. J Phys Chem Lett 2013; 4:70-77. [PMID: 26291214 DOI: 10.1021/jz3018557] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Motivated by future possibilities to design target molecules for fibrils with diagnostic or therapeutic capability related to amyloidosis diseases, we investigate in this work the dielectric nature of amyloid fibril microenvironments in different binding sites using an optical probe, thioflavin-T (THT), which has been used extensively to stain such fibrils. We study the fibril-environment-induced structural and spectral changes of THT at each binding site and compare the results to the fibril-free situation in aqueous solution. All binding sites are found to show a similar effect with respect to the conformational changes of THT; in the presence of the fibril, its molecular geometry tends to become planarized. However, depending on the dielectric nature of the specific binding site, a red shift, blue shift, or no shift in the absorption spectra of THT is predicted. Interestingly, the experimentally measured red shift in the spectra is seen only when THT binds to one of the core or surface-binding sites. It is found that the dielectric nature of the microenvironment in the fibril is strongly nonhomogeneous.
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Affiliation(s)
- N Arul Murugan
- †Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Jógvan Magnus Haugaard Olsen
- ‡Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- ‡Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Zilvinas Rinkevicius
- †Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Kestutis Aidas
- §Department of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Sauletekio al. 9, LT-10222 Vilnius, Lithuania
| | - Hans Ågren
- †Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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30
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Jameson LP, Smith NW, Dzyuba SV. Dye-binding assays for evaluation of the effects of small molecule inhibitors on amyloid (aβ) self-assembly. ACS Chem Neurosci 2012; 3:807-19. [PMID: 23173064 DOI: 10.1021/cn300076x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Dye-binding assays, such as those utilizing Congo red and thioflavin T, are among the most widely used tools to probe the aggregation of amyloidogenic biomolecules and for the evaluation of small molecule inhibitors of amyloid aggregation and fibrillization. A number of recent reports have indicated that these dye-binding assays could be prone to false positive effects when assessing inhibitors' potential toward Aβ peptides, species involved in Alzheimer's disease. Specifically, this review focuses on the application of thioflavin T for determining the efficiency of small molecule inhibitors of Aβ aggregation and addresses potential reasons that might be associated with the false positive effects in an effort to increase reliability of dye-binding assays.
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Affiliation(s)
- Laramie P. Jameson
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Nicholas W. Smith
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Sergei V. Dzyuba
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, United States
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31
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Merlo S, Barillaro G, Carpignano F, Silva G, Surdo S, Strambini LM, Giorgetti S, Nichino D, Relini A, Mazzini G, Stoppini M, Bellotti V. Fibrillogenesis of human β2 -microglobulin in three-dimensional silicon microstructures. JOURNAL OF BIOPHOTONICS 2012; 5:785-792. [PMID: 22271711 DOI: 10.1002/jbio.201100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/03/2012] [Accepted: 01/04/2012] [Indexed: 05/31/2023]
Abstract
The authors describe the interaction of biological nanostructures formed by β(2) -microglobulin amyloid fibrils with three-dimensional silicon microstructures consisting in periodic arrays of vertical silicon walls (≈3 μm-thick) separated by 50 μm-deep air gaps (≈5 μm-wide). These structures are of great interest from a biological point of view since they well mimic the interstitial environment typical of amyloid deposition in vivo. Moreover, they behave as hybrid photonic crystals, potentially applicable as optical transducers for label-free detection of the kinetics of amyloid fibrils formation. Fluorescence and atomic force microscopy (AFM) show that a uniform distribution of amyloid fibrils is achieved when fibrillogenesis occurs directly on silicon. The high resolution AFM images also demonstrate that amyloid fibrils grown on silicon are characterized by the same fine structure typically ensured by fibrillogenesis in solution.
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Affiliation(s)
- Sabina Merlo
- Dipartimento di Elettronica, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy.
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32
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Engel MFM, vandenAkker CC, Schleeger M, Velikov KP, Koenderink GH, Bonn M. The Polyphenol EGCG Inhibits Amyloid Formation Less Efficiently at Phospholipid Interfaces than in Bulk Solution. J Am Chem Soc 2012; 134:14781-8. [DOI: 10.1021/ja3031664] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | | | - Michael Schleeger
- FOM Institute AMOLF, Science Park 104,
1098 XG, Amsterdam, The Netherlands
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
| | - Krassimir P. Velikov
- Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3133 AT Vlaardingen, The Netherlands
- Soft Condensed
Matter, Debye
Institute for Nanomaterials Science, Department of Physics and Astronomy, Utrecht University, Princetonplein 5, 3584 CC, Utrecht,
The Netherlands
| | | | - Mischa Bonn
- FOM Institute AMOLF, Science Park 104,
1098 XG, Amsterdam, The Netherlands
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg
10, 55128 Mainz, Germany
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