1
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Chowdhury S, Sarkar N. Exploring the potential of amyloids in biomedical applications: A review. Biotechnol Bioeng 2024; 121:26-38. [PMID: 37822225 DOI: 10.1002/bit.28569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/13/2023]
Abstract
Amyloid is defined as a fibrous quaternary structure formed by assembling protein or peptide monomers into intermolecularly hydrogen linked β-sheets. There is a prevalent issue with protein aggregation and the buildup of amyloid molecules, which results in human neurological illnesses including Alzheimer's and Parkinson's. But it is now evident that many organisms, like bacteria, fungi as well as humans, use the same fibrillar structure to carry out a variety of biological functions, such as structure and protection supporting interface transitions and cell-cell recognition, protein control and storage, epigenetic inheritance, and memory. Recent discoveries of self-assembling amyloidogenic peptides and proteins, based on the amyloid core structure, give rise to interesting biomaterials with potential uses in numerous industries. These functions dramatically diverge from the initial conception of amyloid fibrils as intrinsically diseased entities. Apart from the natural ability of amyloids to spontaneously arrange themselves and their exceptional material characteristics, this aspect has prompted extensive research into engineering artificial amyloids for generating various nanostructures, molecular substances, and combined materials. Here, we discuss significant developments in the artificial design of useful amyloids as well as how amyloid materials serve as examples of how function emerges from protein self-assembly at various length scales.
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Affiliation(s)
- Srijita Chowdhury
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India
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2
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van Dalen M, Karperien M, Claessens MM, Post JN. Choice of Protein, Not Its Amyloid-Fold, Determines the Success of Amyloid-Based Scaffolds for Cartilage Tissue Regeneration. ACS OMEGA 2023; 8:24198-24209. [PMID: 37457450 PMCID: PMC10339334 DOI: 10.1021/acsomega.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/18/2023] [Indexed: 07/18/2023]
Abstract
The formation of fibrocartilage during articular cartilage regeneration remains a clinical problem affecting adequate restoration of articular cartilage in joints. To stimulate chondrocytes to form articular cartilage, we investigated the use of amyloid fibril-based scaffolds. The proteins α-synuclein, β-lactoglobulin, and lysozyme were induced to self-assemble into amyloid fibrils and, during dialysis, formed micrometer scale amyloid networks that resemble the cartilage extracellular matrix. Our results show that lysozyme amyloid micronetworks supported chondrocyte viability and extracellular matrix deposition, while α-synuclein and β-lactoglobulin maintained cell viability. With this study, we not only confirm the possible use of amyloid materials for tissue regeneration but also demonstrate that the choice of protein, rather than its amyloid-fold per se, affects the cellular response and tissue formation.
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Affiliation(s)
- Maurice
C.E. van Dalen
- Developmental
BioEngineering, TechMed Centre, University
of Twente, Enschede, Overijssel 7500 AE, The Netherlands
- Nanobiophysics,
Mesa+, University of Twente, Enschede 7500AE, The Netherlands
| | - Marcel Karperien
- Developmental
BioEngineering, TechMed Centre, University
of Twente, Enschede, Overijssel 7500 AE, The Netherlands
| | | | - Janine N. Post
- Developmental
BioEngineering, TechMed Centre, University
of Twente, Enschede, Overijssel 7500 AE, The Netherlands
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3
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Vaneyck J, Yousif TA, Segers-Nolten I, Blum C, Claessens MMAE. Quantitative Seed Amplification Assay: A Proof-of-Principle Study. J Phys Chem B 2023; 127:1735-1743. [PMID: 36795058 PMCID: PMC9986870 DOI: 10.1021/acs.jpcb.2c08326] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Amyloid fibrils of the protein α-synuclein (αS) have recently been identified as a biomarker for Parkinson's disease (PD). To detect the presence of these amyloid fibrils, seed amplification assays (SAAs) have been developed. SAAs allow for the detection of αS amyloid fibrils in biomatrices such as cerebral spinal fluid and are promising for PD diagnosis by providing a dichotomous (yes/no) response. The additional quantification of the number of αS amyloid fibrils may enable clinicians to evaluate and follow the disease progression and severity. Developing quantitative SAAs has been shown to be challenging. Here, we report on a proof-of-principle study on the quantification of αS fibrils in fibril-spiked model solutions of increasing compositional complexity including blood serum. We show that parameters derived from standard SAAs can be used for fibril quantification in these solutions. However, interactions between the monomeric αS reactant that is used for amplification and biomatrix components such as human serum albumin have to be taken into account. We demonstrate that quantification of fibrils is possible even down to the single fibril level in a model sample consisting of fibril-spiked diluted blood serum.
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Affiliation(s)
- Jonathan Vaneyck
- Nanobiophysics (NBP), Faculty of Science and Technology, MESA + Institute for Nanotechnology and Technical Medical Centre, University of Twente, PO Box 217, 7500 AE Enschede, Overijssel, The Netherlands
| | - Therese A Yousif
- Nanobiophysics (NBP), Faculty of Science and Technology, MESA + Institute for Nanotechnology and Technical Medical Centre, University of Twente, PO Box 217, 7500 AE Enschede, Overijssel, The Netherlands
| | - Ine Segers-Nolten
- Nanobiophysics (NBP), Faculty of Science and Technology, MESA + Institute for Nanotechnology and Technical Medical Centre, University of Twente, PO Box 217, 7500 AE Enschede, Overijssel, The Netherlands
| | - Christian Blum
- Nanobiophysics (NBP), Faculty of Science and Technology, MESA + Institute for Nanotechnology and Technical Medical Centre, University of Twente, PO Box 217, 7500 AE Enschede, Overijssel, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics (NBP), Faculty of Science and Technology, MESA + Institute for Nanotechnology and Technical Medical Centre, University of Twente, PO Box 217, 7500 AE Enschede, Overijssel, The Netherlands
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4
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Skamris T, Vestergaard B, Madsen KL, Langkilde AE, Foderà V. Identifying Biological and Biophysical Features of Different Maturation States of α-Synuclein Amyloid Fibrils. Methods Mol Biol 2023; 2551:321-344. [PMID: 36310213 DOI: 10.1007/978-1-0716-2597-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein aggregates, hereunder amyloid fibrils, can undergo a maturation process, whereby early formed aggregates undergo a structural and physicochemical transition leading to more mature species. In the case of amyloid-related diseases, such maturation confers distinctive biological properties of the aggregates, which may account for a range of diverse pathological subtypes. Here, we present a protocol for the preparation of α-synuclein amyloid fibrils differing in the level of their maturation. We utilize widely accessible biophysical techniques to characterize the structure and morphology and a simple thermal treatment procedure to test their thermodynamic stability. Their biological properties are probed by means of binding to native plasma membrane sheets originating from mammalian cell lines.
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Affiliation(s)
- Thomas Skamris
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth L Madsen
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Annette E Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - Vito Foderà
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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5
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Seetaloo N, Zacharopoulou M, Stephens AD, Kaminski Schierle GS, Phillips JJ. Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry Approach to Correlate Local Structure and Aggregation in α-Synuclein. Anal Chem 2022; 94:16711-16719. [DOI: 10.1021/acs.analchem.2c03183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Neeleema Seetaloo
- Living Systems Institute, University of Exeter, Stocker Road, ExeterEX4 4QD, U.K
| | - Maria Zacharopoulou
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, CambridgeCB3 0AS, U.K
| | - Amberley D. Stephens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, CambridgeCB3 0AS, U.K
| | - Gabriele S. Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, CambridgeCB3 0AS, U.K
| | - Jonathan J. Phillips
- Living Systems Institute, University of Exeter, Stocker Road, ExeterEX4 4QD, U.K
- Alan Turing Institute, British Library, LondonNW1 2DB, U.K
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6
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Iyer A, Sidhu A, Subramaniam V. How important is the N-terminal acetylation of alpha-synuclein for its function and aggregation into amyloids? Front Neurosci 2022; 16:1003997. [PMID: 36466161 PMCID: PMC9709446 DOI: 10.3389/fnins.2022.1003997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
N-α-acetylation is a frequently occurring post-translational modification in eukaryotic proteins. It has manifold physiological consequences on the regulation and function of several proteins, with emerging studies suggesting that it is a global regulator of stress responses. For decades, in vitro biochemical investigations into the precise role of the intrinsically disordered protein alpha-synuclein (αS) in the etiology of Parkinson's disease (PD) were performed using non-acetylated αS. The N-terminus of α-synuclein is now unequivocally known to be acetylated in vivo, however, there are many aspects of this post-translational modifications that are not understood well. Is N-α-acetylation of αS a constitutive modification akin to most cellular proteins, or is it spatio-temporally regulated? Is N-α-acetylation of αS relevant to the as yet elusive function of αS? How does the N-α-acetylation of αS influence the aggregation of αS into amyloids? Here, we provide an overview of the current knowledge and discuss prevailing hypotheses on the impact of N-α-acetylation of αS on its conformational, oligomeric, and fibrillar states. The extent to which N-α-acetylation of αS is vital for its function, membrane binding, and aggregation into amyloids is also explored here. We further discuss the overall significance of N-α-acetylation of αS for its functional and pathogenic implications in Lewy body formation and synucleinopathies.
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Affiliation(s)
- Aditya Iyer
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arshdeep Sidhu
- Nitte University Centre for Science Education and Research, Nitte University (DU), Mangalore, India
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7
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Vaneyck J, Segers-Nolten I, Broersen K, Claessens MMAE. Cross-seeding of alpha-synuclein aggregation by amyloid fibrils of food proteins. J Biol Chem 2021; 296:100358. [PMID: 33539920 PMCID: PMC7949133 DOI: 10.1016/j.jbc.2021.100358] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 01/22/2023] Open
Abstract
The aggregation of the protein α-synuclein (aSyn) into amyloid fibrils in the human brain is associated with the development of several neurodegenerative diseases, including Parkinson's disease. The previously observed prion-like spreading of aSyn aggregation throughout the brain and the finding that heterologous cross-seeding of amyloid aggregation occurs in vitro for some proteins suggest that exposure to amyloids in general may pose a risk for disease development. To elucidate which protein fibril characteristics determine if and how heterologous amyloid seeding can occur, we investigated the potential of amyloid fibrils formed from proteins found in food, hen egg white lysozyme, and bovine milk β-lactoglobulin to cross-seed aSyn aggregation in the test tube. We observed that amyloid fibrils from lysozyme, but not β-lactoglobulin, potently cross-seeded the aggregation of aSyn as indicated by a significantly shorter lag phase of aSyn aggregation in the presence of lysozyme fibrils. The cross-seeding effect of lysozyme was found to be primarily driven by a surface-mediated nucleation mechanism. The differential seeding effect of lysozyme and β-lactoglobulin on aSyn aggregation could be explained on the basis of binding affinity, binding site, and electrostatic interactions. Our results indicate that heterologous seeding of proteins may occur depending on the physicochemical characteristics of the seed protein fibril. Our findings suggest that heterologous seeding has the potential to determine the pathogenesis of neurodegenerative amyloid diseases.
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Affiliation(s)
- Jonathan Vaneyck
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, Enschede, the Netherlands.
| | - Ine Segers-Nolten
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, Enschede, the Netherlands
| | - Kerensa Broersen
- Applied Stem Cell Technologies, Technical Medical Centre, University of Twente, Enschede, the Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, Enschede, the Netherlands
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8
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Lin X, Galaqin N, Tainaka R, Shimamori K, Kuragano M, Noguchi TQP, Tokuraku K. Real-Time 3D Imaging and Inhibition Analysis of Various Amyloid Aggregations Using Quantum Dots. Int J Mol Sci 2020; 21:E1978. [PMID: 32183170 PMCID: PMC7139405 DOI: 10.3390/ijms21061978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/01/2020] [Accepted: 03/11/2020] [Indexed: 02/07/2023] Open
Abstract
Amyloidosis refers to aggregates of protein that accumulate and are deposited as amyloid fibrils into plaques. When these are detected in organs, they are the main hallmark of Alzheimer's disease, Parkinson's disease, and other related diseases. Recent medical advances have shown that many precursors and proteins can induce amyloidosis even though the mechanism of amyloid aggregation and the relationship of these proteins to amyloidosis remains mostly unclear. In this study, we report the real-time 3D-imaging and inhibition analysis of amyloid β (Aβ), tau, and α-synuclein aggregation utilizing the affinity between quantum dots (QD) and amyloid aggregates. We successfully visualized these amyloid aggregations in real-time using fluorescence microscopy and confocal microscopy simply by adding commercially available QD. The observation by transmission electron microscopy (TEM) showed that QD particles bound to all amyloid fibrils. The 3D-imaging with QD revealed differences between amyloid aggregates composed of different amyloid peptides that could not be detected by TEM. We were also able to quantify the inhibition activities of these proteins by rosmarinic acid, which has high activity for Aβ aggregation, from fluorescence micrographs as half-maximal effective concentrations. These imaging techniques with QD serve as quick, easy, and powerful tools to understand amyloidosis and to discover drugs for therapies.
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Affiliation(s)
- Xuguang Lin
- Department of Applied Science and Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan; (X.L.); (N.G.); (R.T.); (K.S.); (M.K.)
| | - Nuomin Galaqin
- Department of Applied Science and Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan; (X.L.); (N.G.); (R.T.); (K.S.); (M.K.)
| | - Reina Tainaka
- Department of Applied Science and Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan; (X.L.); (N.G.); (R.T.); (K.S.); (M.K.)
| | - Keiya Shimamori
- Department of Applied Science and Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan; (X.L.); (N.G.); (R.T.); (K.S.); (M.K.)
| | - Masahiro Kuragano
- Department of Applied Science and Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan; (X.L.); (N.G.); (R.T.); (K.S.); (M.K.)
| | - Taro Q. P. Noguchi
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, Miyakonojo 885-8567, Japan;
| | - Kiyotaka Tokuraku
- Department of Applied Science and Engineering, Muroran Institute of Technology, Muroran 050-8585, Japan; (X.L.); (N.G.); (R.T.); (K.S.); (M.K.)
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9
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Marczynski M, Rickert CA, Semerdzhiev SA, van Dijk WR, Segers-Nolten IMJ, Claessens MMAE, Lieleg O. α-Synuclein Penetrates Mucin Hydrogels Despite Its Mucoadhesive Properties. Biomacromolecules 2019; 20:4332-4344. [DOI: 10.1021/acs.biomac.9b00905] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Matthias Marczynski
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Garching 85748, Germany
| | - Carolin A. Rickert
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Garching 85748, Germany
| | - Slav A. Semerdzhiev
- Nanobiophysics, Faculty of Science and Technology, University of Twente, Enschede 7522NB, The Netherlands
| | - Wouter R. van Dijk
- Nanobiophysics, Faculty of Science and Technology, University of Twente, Enschede 7522NB, The Netherlands
| | - Ine M. J. Segers-Nolten
- Nanobiophysics, Faculty of Science and Technology, University of Twente, Enschede 7522NB, The Netherlands
| | | | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Garching 85748, Germany
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10
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de Oliveira GAP, Silva JL. Alpha-synuclein stepwise aggregation reveals features of an early onset mutation in Parkinson's disease. Commun Biol 2019; 2:374. [PMID: 31633065 PMCID: PMC6789109 DOI: 10.1038/s42003-019-0598-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/04/2019] [Indexed: 02/08/2023] Open
Abstract
Amyloid formation is a process involving interconverting protein species and results in toxic oligomers and fibrils. Aggregated alpha-synuclein (αS) participates in neurodegenerative maladies, but a closer understanding of the early αS polymerization stages and polymorphism of heritable αS variants is sparse still. Here, we distinguished αS oligomer and protofibril interconversions in Thioflavin T polymerization reactions. The results support a hypothesis reconciling the nucleation-polymerization and nucleation-conversion-polymerization models to explain the dissimilar behaviors of wild-type and the A53T mutant. Cryo-electron microscopy with a direct detector shows the polymorphic nature of αS fibrils formed by heritable A30P, E46K, and A53T point mutations. By showing that A53T rapidly nucleates competent species, continuously elongates fibrils in the presence of increasing amounts of seeds, and overcomes wild-type surface requirements for growth, our findings place A53T with features that may explain the early onset of familial Parkinson's disease cases bearing this mutation.
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Affiliation(s)
- Guilherme A. P. de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901 Brazil
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22904 USA
| | - Jerson L. Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-901 Brazil
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11
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Iyer A, Claessens MMAE. Disruptive membrane interactions of alpha-synuclein aggregates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:468-482. [PMID: 30315896 DOI: 10.1016/j.bbapap.2018.10.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/14/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022]
Abstract
Alpha synuclein (αS) is a ~14 kDa intrinsically disordered protein. Decades of research have increased our knowledge on αS yet its physiological function remains largely elusive. The conversion of monomeric αS into oligomers and amyloid fibrils is believed to play a central role of the pathology of Parkinson's disease (PD). It is becoming increasingly clear that the interactions of αS with cellular membranes are important for both αS's functional and pathogenic actions. Therefore, understanding interactions of αS with membranes seems critical to uncover functional or pathological mechanisms. This review summarizes our current knowledge of how physicochemical properties of phospholipid membranes affect the binding and aggregation of αS species and gives an overview of how post-translational modifications and point mutations in αS affect phospholipid membrane binding and protein aggregation. We discuss the disruptive effects resulting from the interaction of αS aggregate species with membranes and highlight current approaches and hypotheses that seek to understand the pathogenic and/or protective role of αS in PD.
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Affiliation(s)
- Aditya Iyer
- Membrane Enzymology Group, University of Groningen, Groningen 9747 AG, The Netherlands
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12
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Sidhu A, Vaneyck J, Blum C, Segers-Nolten I, Subramaniam V. Polymorph-specific distribution of binding sites determines thioflavin-T fluorescence intensity in α-synuclein fibrils. Amyloid 2018; 25:189-196. [PMID: 30486688 DOI: 10.1080/13506129.2018.1517736] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Thioflavin-T (ThT) is the most commonly used fluorescent dye for following amyloid formation semi-quantitatively in vitro, specifically probing the fibrillar cross-β-sheet content. In recent years, structural polymorphism of amyloid fibrils has been shown to be an important aspect of amyloid formation, both in vitro and in neurodegenerative diseases. Therefore, understanding ThT-amyloid interactions in the context of structural polymorphism of amyloids is necessary for correct interpretation of ThT fluorescence data. Here we study the influence of fibril morphology on ThT fluorescence and ThT binding sites, with two morphologically distinct but chemically identical α-synuclein polymorphs. In ThT fluorescence assays the two polymorphs show type-specific fluorescence intensity behaviour although their β-sheet content has been shown to be similar. Further, fluorescence lifetime measurements of fibril-bound ThT reveal the presence of at least two qualitatively different ThT binding sites on the polymorphs. The relative distributions of the binding sites on the fibril surfaces appear to be morphology dependent, thus determining the observed polymorph-specific ThT fluorescence intensities. These results, highlighting the role of fibril morphology in ThT-based amyloid studies, underline the relevance of polymorphs in ThT-amyloid interaction and can explain the variability often observed in ThT amyloid binding assays.
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Affiliation(s)
- Arshdeep Sidhu
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Jonathan Vaneyck
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Christian Blum
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Ine Segers-Nolten
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands
| | - Vinod Subramaniam
- a Nanobiophysics, MESA + Institute for Nanotechnology, University of Twente , Enschede , The Netherlands.,b Executive Board, Vrije Universiteit Amsterdam , Amsterdam , The Netherlands
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13
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Lee YH, Ramamoorthy A. Semen-derived amyloidogenic peptides-Key players of HIV infection. Protein Sci 2018; 27:1151-1165. [PMID: 29493036 DOI: 10.1002/pro.3395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 12/26/2022]
Abstract
Misfolding and amyloid aggregation of intrinsically disordered proteins (IDPs) are implicated in a variety of diseases. Studies have shown that membrane plays important roles on the formation of intermediate structures of IDPs that can initiate (and/or speed-up) amyloid aggregation to form fibers. The process of amyloid aggregation also disrupts membrane to cause cell death in amyloid diseases like Alzheimer's disease and type-2 diabetes. On the other hand, recent studies reported the membrane fusion properties of amyloid fibers. Remarkably, amyloid-fibril formation by short peptide fragments of highly abundant prostatic acidic-phosphatase (PAP) in human semen and are capable of boosting the rate of HIV infection up to 400,000-fold during sexual contact. Unlike the least toxic fully matured fibers of most amyloid proteins, the semen-derived enhancer of virus infection (SEVI) amyloid-fibrils of PAP peptide fragments are highly potent in rendering the maximum rate of HIV infection. This unusual property of amyloid fibers has witnessed increasing number of studies on the biophysical aspects of fiber formation and fiber-membrane interactions. NMR studies have reported a highly disordered partial helical structure in a membrane environment for the intrinsically disordered PAP peptide that promotes the fusion of the viral membrane with that of host cells. The purpose of this review article is to unify and integrate biophysical and immunological research reported in the previous studies on SEVI. Specifically, amyloid aggregation, dramatic HIV infection enhancing properties, membrane fusion properties, high resolution NMR structure, and approaches to eliminate the enhancement of HIV infection of SEVI peptides are discussed.
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Affiliation(s)
- Young-Ho Lee
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka, 565-0871, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan, 48109-1055
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14
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Iyer A, Roeters SJ, Kogan V, Woutersen S, Claessens MMAE, Subramaniam V. C-Terminal Truncated α-Synuclein Fibrils Contain Strongly Twisted β-Sheets. J Am Chem Soc 2017; 139:15392-15400. [PMID: 28968082 PMCID: PMC5668890 DOI: 10.1021/jacs.7b07403] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
C-terminal truncations
of monomeric wild-type alpha-synuclein (henceforth
WT-αS) have been shown to enhance the formation of amyloid aggregates
both in vivo and in vitro and have
been associated with accelerated progression of Parkinson’s
disease (PD). The correlation with PD may not solely be a result of
faster aggregation, but also of which fibril polymorphs are preferentially
formed when the C-terminal residues are deleted. Considering that
different polymorphs are known to result in distinct pathologies,
it is important to understand how these truncations affect the organization
of αS into fibrils. Here we present high-resolution microscopy
and advanced vibrational spectroscopy studies that indicate that the
C-terminal truncation variant of αS, lacking residues 109–140
(henceforth referred to as 1–108-αS), forms amyloid fibrils
with a distinct structure and morphology. The 1–108-αS
fibrils have a unique negative circular dichroism band at ∼230
nm, a feature that differs from the canonical ∼218 nm band
usually observed for amyloid fibrils. We show evidence that 1–108-αS
fibrils consist of strongly twisted β-sheets with an increased
inter-β-sheet distance and a higher solvent exposure than WT-αS
fibrils, which is also indicated by the pronounced differences in
the 1D-IR (FTIR), 2D-IR, and vibrational circular dichroism spectra.
As a result of their distinct β-sheet structure, 1–108-αS
fibrils resist incorporation of WT-αS monomers.
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Affiliation(s)
- Aditya Iyer
- Nanoscale Biophysics Group, AMOLF , Science Park 104, Amsterdam 1098 XG, The Netherlands.,Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands
| | - Steven J Roeters
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Vladimir Kogan
- Dannalab BV , Wethouder Beversstraat 185, Enschede 7543 BK, The Netherlands
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands
| | - Vinod Subramaniam
- Nanoscale Biophysics Group, AMOLF , Science Park 104, Amsterdam 1098 XG, The Netherlands.,Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands.,Vrije Universiteit Amsterdam , De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
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15
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Afitska K, Fucikova A, Shvadchak VV, Yushchenko DA. Modification of C Terminus Provides New Insights into the Mechanism of α-Synuclein Aggregation. Biophys J 2017; 113:2182-2191. [PMID: 28939194 DOI: 10.1016/j.bpj.2017.08.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022] Open
Abstract
Aggregation of neuronal protein α-synuclein leads to the formation of amyloid fibrils, which are associated with the development of Parkinson's disease. The mechanism of α-synuclein pathology is not fully understood and is a subject of active research in the field. To tackle this problem, the fusions of fluorescent proteins to α-synuclein C-terminus are often used in cellular and animal studies. The effects induced by such α-synuclein sequence extension on α-synuclein aggregation propensity are, however, not systematically examined despite the evidence that the negatively charged C-terminus plays a critical role in the regulation of α-synuclein aggregation. In this work, we investigated how the charge and length variations of the C-terminus affect the aggregation propensity of α-synuclein. To address these questions, we prepared mutants of α-synuclein carrying additional moieties of different charge and length at the protein C-terminus. We determined the rates of two different aggregation stages (primary nucleation and elongation) based on a thioflavin T kinetic assay. We observed that all mutants bearing neutrally charged moieties of different length fibrilized slower than wild-type α-synuclein. The primary nucleation and elongation rates strongly decreased with increase of the C-terminal extension length. Meanwhile, charge variation of the C-terminus significantly changed the rate of α-synuclein nucleation, but did not markedly affect the rate of fibril elongation. Our data demonstrate that both the charge and length of the C-terminus play an important role at the stage of initial fibril formation, but the stage of fibril elongation is affected mainly by the length of C-terminal extension. In addition, our results suggest that there are at least two steps of incorporation of α-synuclein monomers into the amyloid fibril: namely, the initial monomer binding to the fibril end (charge-dependent, relatively fast), and the subsequent conformational change of the protein (charge-independent, relatively slow, and thus the rate-limiting step).
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Affiliation(s)
- Kseniia Afitska
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anna Fucikova
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Volodymyr V Shvadchak
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dmytro A Yushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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16
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Semerdzhiev SA, Shvadchak VV, Subramaniam V, Claessens MMAE. Non-uniform self-assembly: On the anisotropic architecture of α-synuclein supra-fibrillar aggregates. Sci Rep 2017; 7:7699. [PMID: 28794461 PMCID: PMC5550477 DOI: 10.1038/s41598-017-06532-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/14/2017] [Indexed: 11/09/2022] Open
Abstract
Although the function of biopolymer hydrogels in nature depends on structural anisotropy at mesoscopic length scales, the self-assembly of such anisotropic structures in vitro is challenging. Here we show that fibrils of the protein α-synuclein spontaneously self-assemble into structurally anisotropic hydrogel particles. While the fibrils in the interior of these supra-fibrillar aggregates (SFAs) are randomly oriented, the fibrils in the periphery prefer to cross neighboring fibrils at high angles. This difference in organization coincides with a significant difference in polarity of the environment in the central and peripheral parts of the SFA. We rationalize the structural anisotropy of SFAs in the light of the observation that αS fibrils bind a substantial amount of counterions. We propose that, with the progress of protein polymerization into fibrils, this binding of counterions changes the ionic environment which triggers a change in fibril organization resulting in anisotropy in the architecture of hydrogel particles.
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Affiliation(s)
- Slav A Semerdzhiev
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands
| | - Volodymyr V Shvadchak
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, 166-10, Czech Republic
| | - Vinod Subramaniam
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands.
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17
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Bloch D, Miller Y. Study of Molecular Mechanisms of α-Synuclein Assembly: Insight into a Cross-β Structure in the N-Termini of New α-Synuclein Fibrils. ACS OMEGA 2017; 2:3363-3370. [PMID: 30023693 PMCID: PMC6044890 DOI: 10.1021/acsomega.7b00459] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/26/2017] [Indexed: 06/08/2023]
Abstract
Parkinson's disease is characterized by the self-assembly of α-synuclein (AS), in which its aggregates accumulate in the substantia nigra. The molecular mechanisms of the self-assembly of AS are challenging because AS is a relatively large intrinsically disordered protein, consisting of 140 residues. It is known that the N-termini of AS contribute to the toxicity of the proteins; therefore, it is important to investigate the self-assembly structure of the N-termini on AS as well. There have been extensive efforts to investigate the structural fibrils of AS(1-140), which have shown that the N-termini are disordered and do not participate in the fibrillary structure. This study illustrates for the first time that the N-termini of AS play a crucial role in the self-assembly of AS. This study reveals a new structure of AS(1-140) fibrils, in which the N-termini are essential parts of the cross-β structure of the fibrillary structure. This study suggests that there are polymorphic states of the self-assembled AS(1-140). While the polymorphic states of the N-termini do not participate in the fibrillary structure and fluctuate, our predicted new fibrillary structure of the N-termini not only participates in the fibrillary structure but also stabilizes the fibrillary structure.
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Affiliation(s)
- Daniel
Nir Bloch
- Department
of Chemistry and Ilse Katz Institute for Nanoscale Science
and Technology, Ben-Gurion University of
the Negev, Beer-Sheva 84105, Israel
| | - Yifat Miller
- Department
of Chemistry and Ilse Katz Institute for Nanoscale Science
and Technology, Ben-Gurion University of
the Negev, Beer-Sheva 84105, Israel
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18
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Chaudhary H, Subramaniam V, Claessens MMAE. Direct Visualization of Model Membrane Remodeling by α-Synuclein Fibrillization. Chemphyschem 2017; 18:1620-1626. [PMID: 28370874 PMCID: PMC5485007 DOI: 10.1002/cphc.201700050] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/03/2022]
Abstract
The interaction of α‐synuclein (αS) with membranes is thought to be critical in the etiology of Parkinson's disease. Besides oligomeric αS aggregates that possibly form membrane pores, the aggregation of αS into amyloid fibrils has been reported to disrupt membranes. The mechanism by which aggregation affects the integrity of membranes is, however, unknown. Here, we show that whereas mature αS fibrils only weakly adhere to POPC/POPG giant unilamellar vesicles (GUVs), fibrillization of αS on the membrane results in large‐scale membrane remodeling. Fibrils that grow on the vesicle surface stiffen the membrane and make the initially spherical membrane become polyhedral. Additionally, membrane‐attached fibrils extract lipids. The lipid extraction and membrane remodeling of growing fibrils can consume the complete bilayer surface and results in loss of vesicle content. These observations suggest that there are several mechanisms by which growing fibrils can disrupt membrane function.
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Affiliation(s)
- Himanshu Chaudhary
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500AE, Enschede, The Netherlands
| | - Vinod Subramaniam
- Vrije Universiteit Amsterdam, De Boelelaan 1104, 1081HV, Amsterdam, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500AE, Enschede, The Netherlands
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19
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Sidhu A, Segers-Nolten I, Raussens V, Claessens MMAE, Subramaniam V. Distinct Mechanisms Determine α-Synuclein Fibril Morphology during Growth and Maturation. ACS Chem Neurosci 2017; 8:538-547. [PMID: 28292187 DOI: 10.1021/acschemneuro.6b00287] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Amyloid polymorphs have become one of the focal points of molecular studies of neurodegenerative diseases like Parkinson's disease. Due to their distinct biochemical properties and prion-like characteristics, insights into the molecular origin and stability of amyloid polymorphs over time are crucial for understanding the potential role of amyloid polymorphism in these diseases. Here, we systematically study the fibrillization of recombinantly produced human α-synuclein (αSyn) over an extended period of time to unravel the origin and temporal evolution of polymorphism. We follow morphological changes in the same fibril sample with atomic force microscopy over a period of 1 year. We show that wild-type (wt) αSyn fibrils undergo a slow maturation over time after reaching the plateau phase of aggregation (as detected in a Thioflavin-T fluorescence assay). This maturation, visualized by changes in the fibril periodicity over time, is absent in the disease mutant fibrils. The β-sheet content of the plateau phase and matured fibrils, obtained using Fourier transform infrared spectroscopy, is however similar for the αSyn protein sequences, suggesting that the morphological changes in wt αSyn fibrils are tertiary or quaternary in origin. Furthermore, results from a reversibility assay show that the plateau phase fibrils do not disassemble over time. Together, the observed changes in the periodicity distributions and stability of the fibrillar core over time point toward two distinct mechanisms that determine the morphology of wt αSyn fibrils: competitive growth between different polymorphs during the fibrillization phase followed by a process wherein fibrils undergo slow maturation or annealing.
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Affiliation(s)
- Arshdeep Sidhu
- Nanobiophysics,
MESA+ Institute for Nanotechnology, University of Twente, Postbox 217, 7500 AE Enschede, The Netherlands
| | - Ine Segers-Nolten
- Nanobiophysics,
MESA+ Institute for Nanotechnology, University of Twente, Postbox 217, 7500 AE Enschede, The Netherlands
| | - Vincent Raussens
- Structural
Biology and Bioinformatics Centre, Structure and Function of Biological
Membranes, Faculty of Science, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Mireille M. A. E. Claessens
- Nanobiophysics,
MESA+ Institute for Nanotechnology, University of Twente, Postbox 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente, Postbox 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics,
MESA+ Institute for Nanotechnology, University of Twente, Postbox 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente, Postbox 217, 7500 AE Enschede, The Netherlands
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
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20
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Makky A, Bousset L, Polesel-Maris J, Melki R. Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein. Sci Rep 2016; 6:37970. [PMID: 27901068 PMCID: PMC5128817 DOI: 10.1038/srep37970] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/03/2016] [Indexed: 11/17/2022] Open
Abstract
Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson's disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young's modulus).
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Affiliation(s)
- Ali Makky
- Institut Galien Paris-Sud, CNRS, Univ. Paris-Sud, University Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Luc Bousset
- Paris-Saclay Institute of Neuroscience, Centre National de la Recherche Scientifique, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Jérôme Polesel-Maris
- Luxembourg Institute of Science and Technology (LIST), Materials Research and Technology (MRT), L-4422 Belvaux, Luxembourg
| | - Ronald Melki
- Paris-Saclay Institute of Neuroscience, Centre National de la Recherche Scientifique, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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21
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Timesaving microwave assisted synthesis of insulin amyloid fibrils with enhanced nanofiber aspect ratio. Int J Biol Macromol 2016; 92:225-231. [DOI: 10.1016/j.ijbiomac.2016.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/11/2016] [Accepted: 07/02/2016] [Indexed: 01/23/2023]
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22
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Iyer A, Roeters SJ, Schilderink N, Hommersom B, Heeren RMA, Woutersen S, Claessens MMAE, Subramaniam V. The Impact of N-terminal Acetylation of α-Synuclein on Phospholipid Membrane Binding and Fibril Structure. J Biol Chem 2016; 291:21110-21122. [PMID: 27531743 PMCID: PMC5076520 DOI: 10.1074/jbc.m116.726612] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Indexed: 11/29/2022] Open
Abstract
Human α-synuclein (αS) has been shown to be N terminally acetylated in its physiological state. This modification is proposed to modulate the function and aggregation of αS into amyloid fibrils. Using bacterially expressed acetylated-αS (NTAc-αS) and endogenous αS (Endo-αS) from human erythrocytes, we show that N-terminal acetylation has little impact on αS binding to anionic membranes and thus likely not relevant for regulating membrane affinity. N-terminal acetylation does have an effect on αS aggregation, resulting in a narrower distribution of the aggregation lag times and rates. 2D-IR spectra show that acetylation changes the secondary structure of αS in fibrils. This difference may arise from the slightly higher helical propensity of acetylated-αS in solution leading to a more homogenous fibril population with different fibril structure than non-acetylated αS. We speculate that N-terminal acetylation imposes conformational restraints on N-terminal residues in αS, thus predisposing αS toward specific interactions with other binding partners or alternatively decrease nonspecific interactions.
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Affiliation(s)
- Aditya Iyer
- From the Nanoscale Biophysics Group, FOM Institute AMOLF, Amsterdam, the Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede
| | - Steven J Roeters
- the Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam
| | - Nathalie Schilderink
- the Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede
| | - Bob Hommersom
- the BioImaging MS Group, FOM Institute AMOLF, Amsterdam, The Netherlands
| | - Ron M A Heeren
- the BioImaging MS Group, FOM Institute AMOLF, Amsterdam, The Netherlands, the M4I, The Maastricht MultiModal Molecular Imaging Institute, University of Maastricht, and
| | - Sander Woutersen
- the Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam,
| | | | - Vinod Subramaniam
- From the Nanoscale Biophysics Group, FOM Institute AMOLF, Amsterdam, the Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente, Enschede, the Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
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23
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Mučibabić M, Apetri MM, Canters GW, Aartsma TJ. The effect of fluorescent labeling on α-synuclein fibril morphology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1419-27. [PMID: 27475048 DOI: 10.1016/j.bbapap.2016.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/06/2016] [Accepted: 07/21/2016] [Indexed: 11/15/2022]
Abstract
The misfolding and aggregation of a small, natively unfolded protein α-synuclein (α-syn) is presumably an important factor in the development of Parkinson's disease. However, the mechanism of α-syn aggregation into amyloid fibrils and their morphology are not well understood. To elucidate the aggregation kinetics and the morphology of aggregates by the use of fluorescent techniques the protein needs to be suitably labeled. In this study, using atomic force microscopy, we demonstrate a significant effect of fluorescent labels on the α-syn fibrillization process. We studied in detail the morphology of α-syn aggregates as a function of the composition of mixtures of labeled and wild type (WT) α-syn in solution using different types of fluorescent dyes. Although the overall charge of the fluorophores we used and their chemical structure varied significantly, the morphology of α-syn fibrils changed in a similar way in all cases. The increase in the fraction of labeled α-syn in solution led to shortening of the fibrils as compared to those from WT-only α-syn, whereas the height of the fibrils remained mainly unaffected. The twisted fibril morphology observed in the WT and A140C α-syn mutant completely disappeared when the A140C α-syn mutant was 100% fluorescently labeled.
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Affiliation(s)
- M Mučibabić
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - M M Apetri
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - G W Canters
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - T J Aartsma
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
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24
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Sidhu A, Segers-Nolten I, Subramaniam V. Conformational Compatibility Is Essential for Heterologous Aggregation of α-Synuclein. ACS Chem Neurosci 2016; 7:719-27. [PMID: 26996749 DOI: 10.1021/acschemneuro.5b00322] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Under aggregation-prone conditions, soluble amyloidogenic protein monomers can self-assemble into fibrils or they can fibrillize on preformed fibrillar seeds (seeded aggregation). Seeded aggregations are known to propagate the morphology of the seeds in the event of cross-seeding. However, not all proteins are known to cross-seed aggregation. Cross-seeding has been proposed to be restricted either because of differences in the protein sequences or because of conformations between the seeds and the soluble monomers. Here, we examine cross-seeding efficiency between three α-synuclein sequences, wild-type, A30P, and A53T, each varying in only one or two amino acids but forming morphologically distinct fibrils. Results from bulk Thioflavin-T measurements, monomer incorporation quantification, single fibril fluorescence microscopy, and atomic force microscopy show that under the given solution conditions conformity between the conformation of seeds and monomers is essential for seed elongation. Moreover, elongation characteristics of the seeds are defined by the type of seed.
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Affiliation(s)
| | | | - Vinod Subramaniam
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
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25
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Direct Observation of α-Synuclein Amyloid Aggregates in Endocytic Vesicles of Neuroblastoma Cells. PLoS One 2016; 11:e0153020. [PMID: 27105068 PMCID: PMC4841506 DOI: 10.1371/journal.pone.0153020] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
Aggregation of α-synuclein has been linked to both familial and sporadic Parkinson's disease. Recent studies suggest that α-synuclein aggregates may spread from cell to cell and raise questions about the propagation of neurodegeneration. While continuous progress has been made characterizing α-synuclein aggregates in vitro, there is a lack of information regarding the structure of these species inside the cells. Here, we use confocal fluorescence microscopy in combination with direct stochastic optical reconstruction microscopy, dSTORM, to investigate α-synuclein uptake when added exogenously to SH-SY5Y neuroblastoma cells, and to probe in situ morphological features of α-synuclein aggregates with near nanometer resolution. We demonstrate that using dSTORM, it is possible to follow noninvasively the uptake of extracellularly added α-synuclein aggregates by the cells. Once the aggregates are internalized, they move through the endosomal pathway and accumulate in lysosomes to be degraded. Our dSTORM data show that α-synuclein aggregates remain assembled after internalization and they are shortened as they move through the endosomal pathway. No further aggregation was observed inside the lysosomes as speculated in the literature, nor in the cytoplasm of the cells. Our study thus highlights the super-resolution capability of dSTORM to follow directly the endocytotic uptake of extracellularly added amyloid aggregates and to probe the morphology of in situ protein aggregates even when they accumulate in small vesicular compartments.
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26
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Ilie IM, den Otter WK, Briels WJ. A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation. J Chem Phys 2016; 144:085103. [DOI: 10.1063/1.4942115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Ioana M. Ilie
- Computational Chemical Physics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Wouter K. den Otter
- Computational Chemical Physics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- Multi Scale Mechanics, Faculty of Engineering Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Wim J. Briels
- Computational Chemical Physics, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- Forschungszentrum Jülich, ICS, D-52425 Jülich, Germany
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27
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Wang JJ, Liu GY, Liu G, Zeng QH, Shen X, Hou Y, Li L, Hu SQ. The soluble recombinant N-terminal domain of HMW 1Dx5 and its aggregation behavior. Food Res Int 2015; 78:201-208. [PMID: 28433283 DOI: 10.1016/j.foodres.2015.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/23/2015] [Accepted: 10/06/2015] [Indexed: 12/12/2022]
Abstract
This study seeks to clarify and determine the fundamental properties of N-terminal domain of high molecular weight glutenin subunits (HMW-GS) 1Dx5 (1Dx5-N). 1Dx5-N was expressed in E. coli and its solubility was measured by spectrophotometry. Effects of edible salts (NaCl, Na2CO3), disulfide bond reductant dithiothreitol (DTT) and hydrophobic interactions of denaturant sodium dodecyl sulfonate (SDS) on 1Dx5-N polymer were investigated by native polyacrylamide gelelectrophoresis (PAGE), nonreducing/reducing SDS-PAGE, intrinsic fluorescence, size exclusion chromatography (SEC), dynamic light scattering (DLS) and circular dichroism (CD). Results showed that 1Dx5-N formed a soluble aggregate in aqueous solutions by native-PAGE, clarifying the role of N-terminal of HMW-GS in the insolubility of the whole subunits. Meanwhile, the hydrophobic interaction was more potent in promoting the aggregation of 1Dx5-N in aqueous solutions from the results of SEC, DLS and CD. Edible salts, NaCl and Na2CO3, could improve the polymer formation of 1Dx5-N through disulfide bonds. Moreover, Na2CO3 at high concentrations (>200mM) greatly favored polymer formation by disulfide bonds, and it induced other types of cross-links between amino acids in 1Dx5-N according to nonreducing/reducing SDS-PAGE and fluorescence spectrum. Moreover, the formation of covalent bonds was reinforced by hydrophobic interactions between 1Dx5-N. Therefore, these results provide much novel information on the N-terminal domain of HMW-GS to facilitate the understanding of its functional properties in wheat flour.
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Affiliation(s)
- Jing Jing Wang
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China
| | - Guang-Yi Liu
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China
| | - Guang Liu
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China
| | - Qiao-Hui Zeng
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China
| | - Xing Shen
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China
| | - Yi Hou
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Lin Li
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China; Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Song-Qing Hu
- School of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China; Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, Guangdong 510640, China.
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Stefanovic AND, Lindhoud S, Semerdzhiev SA, Claessens MMAE, Subramaniam V. Oligomers of Parkinson’s Disease-Related α-Synuclein Mutants Have Similar Structures but Distinctive Membrane Permeabilization Properties. Biochemistry 2015; 54:3142-50. [DOI: 10.1021/bi501369k] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anja N. D. Stefanovic
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Saskia Lindhoud
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Slav A. Semerdzhiev
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Mireille M. A. E. Claessens
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- Nanobiophysics,
MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- MIRA
Institute for Biomedical Technology and Technical Medicine, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
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Shvadchak VV, Claessens MMAE, Subramaniam V. Fibril Breaking Accelerates α-Synuclein Fibrillization. J Phys Chem B 2015; 119:1912-8. [DOI: 10.1021/jp5111604] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Volodymyr V. Shvadchak
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
- Nanobiophysics, MESA+ Institute for Nanotechnology & MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
| | - Mireille M. A. E. Claessens
- Nanobiophysics, MESA+ Institute for Nanotechnology & MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
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Povilonienė S, Časaitė V, Bukauskas V, Šetkus A, Staniulis J, Meškys R. Functionalization of α-synuclein fibrils. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:124-33. [PMID: 25671157 PMCID: PMC4311755 DOI: 10.3762/bjnano.6.12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 12/04/2014] [Indexed: 05/05/2023]
Abstract
The propensity of peptides and proteins to form self-assembled structures has very promising applications in the development of novel nanomaterials. Under certain conditions, amyloid protein α-synuclein forms well-ordered structures - fibrils, which have proven to be valuable building blocks for bionanotechnological approaches. Herein we demonstrate the functionalization of fibrils formed by a mutant α-synuclein that contains an additional cysteine residue. The fibrils have been biotinylated via thiol groups and subsequently joined with neutravidin-conjugated gold nanoparticles. Atomic force microscopy and transmission electron microscopy confirmed the expected structure - nanoladders. The ability of fibrils (and of the additional components) to assemble into such complex structures offers new opportunities for fabricating novel hybrid materials or devices.
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Affiliation(s)
- Simona Povilonienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Mokslininku 12, Vilnius LT-08662, Lithuania
| | - Vida Časaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Mokslininku 12, Vilnius LT-08662, Lithuania
| | - Virginijus Bukauskas
- Semiconductor Physics Institute, Center for Physical Sciences and Technology, A. Gostauto 11, Vilnius LT-01108, Lithuania
| | - Arūnas Šetkus
- Semiconductor Physics Institute, Center for Physical Sciences and Technology, A. Gostauto 11, Vilnius LT-01108, Lithuania
| | - Juozas Staniulis
- Institute of Botany of Nature Research Center, Zaliuju Ezeru 49, LT-08406 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Mokslininku 12, Vilnius LT-08662, Lithuania
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