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Kumar V, Sinha N, Thakur AK. Necessity of regulatory guidelines for the development of amyloid based biomaterials. Biomater Sci 2021; 9:4410-4422. [PMID: 34018497 DOI: 10.1039/d1bm00059d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Amyloid diseases are caused due to protein homeostasis failure where incorrectly folded proteins/peptides form cross-β-sheet rich amyloid fibrillar structures. Besides proteins/peptides, small metabolite assemblies also exhibit amyloid-like features. These structures are linked to several human and animal diseases. In addition, non-toxic amyloids with diverse physiological roles are characterized as a new functional class. This finding, along with the unique properties of amyloid like stability and mechanical strength, led to a surge in the development of amyloid-based biomaterials. However, the usage of these materials by humans and animals may pose a health risk such as the development of amyloid diseases and toxicity. This is possible because amyloid-based biomaterials and their fragments may assist seeding and cross-seeding mechanisms of amyloid formation in the body. This review summarizes the potential uses of amyloids as biomaterials, the concerns regarding their usage, and a prescribed workflow to initiate a regulatory approach.
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Affiliation(s)
- Vijay Kumar
- Department of Molecular Microbiology and Biotechnology, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nabodita Sinha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, UP-208016, India.
| | - Ashwani Kumar Thakur
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, UP-208016, India.
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52
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Dean DN, Lee JC. Linking Parkinson's Disease and Melanoma: Interplay Between α-Synuclein and Pmel17 Amyloid Formation. Mov Disord 2021; 36:1489-1498. [PMID: 34021920 DOI: 10.1002/mds.28655] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/22/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder associated with the death of dopaminergic neurons within the substantia nigra of the brain. Melanoma is a cancer of melanocytes, pigmented cells that give rise to skin tone, hair, and eye color. Although these two diseases fundamentally differ, with PD leading to cell degeneration and melanoma leading to cell proliferation, epidemiological evidence has revealed a reciprocal relationship where patients with PD are more susceptible to melanoma and patients with melanoma are more susceptible to PD. The hallmark pathology observed in PD brains is intracellular inclusions, of which the primary component is proteinaceous α-synuclein (α-syn) amyloid fibrils. α-Syn also has been detected in cultured melanoma cells and tissues derived from patients with melanoma, where an inverse correlation exists between α-syn expression and pigmentation. Although this has led to the prevailing hypothesis that α-syn inhibits enzymes involved in melanin biosynthesis, we recently reported an alternative hypothesis in which α-syn interacts with and modulates the aggregation of Pmel17, a functional amyloid that serves as a scaffold for melanin biosynthesis. In this perspective, we review the literature describing the epidemiological and molecular connections between PD and melanoma, presenting both the prevailing hypothesis and our amyloid-centric hypothesis. We offer our views of the essential questions that remain unanswered to motivate future investigations. Understanding the behavior of α-syn in melanoma could not only provide novel approaches for treating melanoma but also could reveal insights into the role of α-syn in PD. © 2021 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Dexter N Dean
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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Abstract
Neurodegenerative disorders are frequently associated with β-sheet-rich amyloid deposits. Amyloid-forming proteins can aggregate under different structural conformations known as strains, which can exhibit a prion-like behavior and distinct pathophenotypes. Precise molecular determinants defining strain specificity and cross-strain interactions (cross-seeding) are currently unknown. The HET-s prion protein from the fungus Podospora anserina represents a model system to study the fundamental properties of prion amyloids. Here, we report the amyloid prion structure of HELLF, a distant homolog of the model prion HET-s. We find that these two amyloids, sharing only 17% sequence identity, have nearly identical β-solenoid folds but lack cross-seeding ability in vivo, indicating that prion specificity can differ in extremely similar amyloid folds. We engineer the HELLF sequence to explore the limits of the sequence-to-fold conservation and to pinpoint determinants of cross-seeding and prion specificity. We find that amyloid fold conservation occurs even at an exceedingly low level of identity to HET-s (5%). Next, we derive a HELLF-based sequence, termed HEC, able to breach the cross-seeding barrier in vivo between HELLF and HET-s, unveiling determinants controlling cross-seeding at residue level. These findings show that virtually identical amyloid backbone structures might not be sufficient for cross-seeding and that critical side-chain positions could determine the seeding specificity of an amyloid fold. Our work redefines the conceptual boundaries of prion strain and sheds light on key molecular features concerning an important class of pathogenic agents.
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Characterization of design grammar of peptides for regulating liquid droplets and aggregates of FUS. Sci Rep 2021; 11:6643. [PMID: 33758287 PMCID: PMC7988016 DOI: 10.1038/s41598-021-86098-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Liquid droplets of aggregation-prone proteins, which become hydrogels or form amyloid fibrils, are a potential target for drug discovery. In this study, we proposed an experiment-guided protocol for characterizing the design grammar of peptides that can regulate droplet formation and aggregation. The protocol essentially involves investigation of 19 amino acid additives and polymerization of the identified amino acids. As a proof of concept, we applied this protocol to fused in sarcoma (FUS). First, we evaluated 19 amino acid additives for an FUS solution and identified Arg and Tyr as suppressors of droplet formation. Molecular dynamics simulations suggested that the Arg additive interacts with specific residues of FUS, thereby inhibiting the cation-π and electrostatic interactions between the FUS molecules. Second, we observed that Arg polymers promote FUS droplet formation, unlike Arg monomers, by bridging the FUS molecules. Third, we found that the Arg additive suppressed solid aggregate formation of FUS, while Arg polymer enhanced it. Finally, we observed that amyloid-forming peptides induced the conversion of FUS droplets to solid aggregates of FUS. The developed protocol could be used for the primary design of peptides controlling liquid droplets and aggregates of proteins.
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55
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Zhang Y, Zhang M, Liu Y, Zhang D, Tang Y, Ren B, Zheng J. Dual amyloid cross-seeding reveals steric zipper-facilitated fibrillization and pathological links between protein misfolding diseases. J Mater Chem B 2021; 9:3300-3316. [PMID: 33651875 DOI: 10.1039/d0tb02958k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amyloid cross-seeding, as a result of direct interaction and co-aggregation between different disease-causative peptides, is considered as a main mechanism for the spread of the overlapping pathology across different cells and tissues between different protein-misfolding diseases (PMDs). Despite the biomedical significance of amyloid cross-seeding in amyloidogenesis, it remains a great challenge to discover amyloid cross-seeding systems and reveal their cross-seeding structures and mechanisms. Herein, we are the first to report that GNNQQNY - a short fragment from yeast prion protein Sup35 - can cross-seed with both amyloid-β (Aβ, associated with Alzheimer's disease) and human islet amyloid polypeptide (hIAPP, associated with type II diabetes) to form β-structure-rich assemblies and to accelerate amyloid fibrillization. Dry, steric β-zippers, formed by the two β-sheets of different amyloid peptides, provide generally interactive and structural motifs to facilitate amyloid cross-seeding. The presence of different steric β-zippers in a variety of GNNQQNY-Aβ and GNNQQNY-hIAPP assemblies also explains amyloid polymorphism. In addition, alteration of steric zipper formation by single-point mutations of GNNQQNY and interactions of GNNQQNY with different Aβ and hIAPP seeds leads to different amyloid cross-seeding efficiencies, further confirming the existence of cross-seeding barriers. This work offers a better structural-based understanding of amyloid cross-seeding mechanisms linked to different PMDs.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering The University of Akron, Ohio, USA.
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56
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 386] [Impact Index Per Article: 128.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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57
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Schimansky A, Yadav JK. Amyloid cross-sequence interaction between Aβ(1-40) and αA(66-80) in relation to the pathogenesis of cataract. Int J Biol Macromol 2021; 179:61-70. [PMID: 33626371 DOI: 10.1016/j.ijbiomac.2021.02.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/29/2021] [Accepted: 02/15/2021] [Indexed: 10/22/2022]
Abstract
Alzheimer's disease (AD) and cataract represent two common protein misfolding diseases closely associated with aging. Growing evidence suggests that these two diseases may be interrelated with each other through cross-sequence interactions between β-amyloid (Aβ) peptide and the short aggregating peptides derived from proteolytic breakdown of α-crystallin. αΑ(66-80) is one of several peptides produced by the proteolytic breakdown of α-crystallin in aged eye lens. Although it is evident that the Aβ(1-40) and αΑ(66-80) coexist in aged eye lenses and both the peptides are known to form macromolecular assemblies, their cross-sequence interaction and the seeding behavior are not known. In this study, the aggregation behavior of αΑ(66-80) has been examined in the presence of Aβ(1-40) on using thioflavin T (ThT) based aggregation kinetics. The presence of monomeric Aβ(1-40) augmented the aggregation kinetics of αΑ(66-80) and reduced the lag time of αΑ(66-80) aggregation. However, the addition of Aβ(1-40) or αΑ(66-80) fibrils (seeds) didn't result in any change in the rate of αΑ(66-80) aggregation. In this in vitro study, we could show that the presence Aβ(1-40) has substantial effect on the aggregation of αΑ(66-80), which suggests a possible interaction between AD and cataract pathologies.
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Affiliation(s)
- Anna Schimansky
- Ulm University, Institute of Protein Biochemistry, Helmholtzstraße 8/1, 89081 Ulm, Germany
| | - Jay Kant Yadav
- Ulm University, Institute of Protein Biochemistry, Helmholtzstraße 8/1, 89081 Ulm, Germany; Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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58
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Lysozyme Fibrils Alter the Mechanism of Insulin Amyloid Aggregation. Int J Mol Sci 2021; 22:ijms22041775. [PMID: 33579016 PMCID: PMC7916790 DOI: 10.3390/ijms22041775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/30/2022] Open
Abstract
Protein aggregation into amyloid fibrils is linked to multiple disorders. The understanding of how natively non-harmful proteins convert to these highly cytotoxic amyloid aggregates is still not sufficient, with new ideas and hypotheses being presented each year. Recently it has been shown that more than one type of protein aggregates may co-exist in the affected tissue of patients suffering from amyloid-related disorders, sparking the idea that amyloid aggregates formed by one protein may induce another protein’s fibrillization. In this work, we examine the effect that lysozyme fibrils have on insulin amyloid aggregation. We show that not only do lysozyme fibrils affect insulin nucleation, but they also alter the mechanism of its aggregation.
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59
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Dangerous Stops: Nonsense Mutations Can Dramatically Increase Frequency of Prion Conversion. Int J Mol Sci 2021; 22:ijms22041542. [PMID: 33546497 PMCID: PMC7913716 DOI: 10.3390/ijms22041542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/26/2022] Open
Abstract
Amyloid formation is associated with many incurable diseases. For some of these, sporadic cases are much more common than familial ones. Some reports point to the role of somatic cell mosaicism in these cases via origination of amyloids in a limited number of cells, which can then spread through tissues. However, specific types of sporadic mutations responsible for such effects are unknown. In order to identify mutations capable of increasing the de novo appearance of amyloids, we searched for such mutants in the yeast prionogenic protein Sup35. We introduced to yeast cells an additional copy of the SUP35 gene with mutated amyloidogenic domain and observed that some nonsense mutations increased the incidence of prions by several orders of magnitude. This effect was related to exposure at the C-terminus of an internal amyloidogenic region of Sup35. We also discovered that SUP35 mRNA could undergo splicing, although inefficiently, causing appearance of a shortened Sup35 isoform lacking its functional domain, which was also highly prionogenic. Our data suggest that truncated forms of amyloidogenic proteins, resulting from nonsense mutations or alternative splicing in rare somatic cells, might initiate spontaneous localized formation of amyloids, which can then spread, resulting in sporadic amyloid disease.
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60
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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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61
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Prabakaran R, Rawat P, Thangakani AM, Kumar S, Gromiha MM. Protein aggregation: in silico algorithms and applications. Biophys Rev 2021; 13:71-89. [PMID: 33747245 PMCID: PMC7930180 DOI: 10.1007/s12551-021-00778-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/01/2021] [Indexed: 01/08/2023] Open
Abstract
Protein aggregation is a topic of immense interest to the scientific community due to its role in several neurodegenerative diseases/disorders and industrial importance. Several in silico techniques, tools, and algorithms have been developed to predict aggregation in proteins and understand the aggregation mechanisms. This review attempts to provide an essence of the vast developments in in silico approaches, resources available, and future perspectives. It reviews aggregation-related databases, mechanistic models (aggregation-prone region and aggregation propensity prediction), kinetic models (aggregation rate prediction), and molecular dynamics studies related to aggregation. With a multitude of prediction models related to aggregation already available to the scientific community, the field of protein aggregation is rapidly maturing to tackle new applications.
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Affiliation(s)
- R. Prabakaran
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - Puneet Rawat
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - A. Mary Thangakani
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceutical Inc., Ridgefield, CT USA
| | - M. Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu India
- School of Computing, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa Japan
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62
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Ivanova MI, Lin Y, Lee YH, Zheng J, Ramamoorthy A. Biophysical processes underlying cross-seeding in amyloid aggregation and implications in amyloid pathology. Biophys Chem 2021; 269:106507. [PMID: 33254009 PMCID: PMC10317075 DOI: 10.1016/j.bpc.2020.106507] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/18/2022]
Abstract
Abnormal aggregation of proteins into filamentous aggregates commonly associates with many diseases, such as Alzheimer's disease, Parkinson's disease and type-2 diabetes. These filamentous aggregates, also known as amyloids, can propagate their abnormal structures to either the same precursor molecules (seeding) or other protein monomers (cross-seeding). Cross-seeding has been implicated in the abnormal protein aggregation and has been found to facilitate the formation of physiological amyloids. It has risen to be an exciting area of research with a high volume of published reports. In this review article, we focus on the biophysical processes underlying the cross-seeding for some of the most commonly studied amyloid proteins. Here we will discuss the relevant literature related to cross-seeded polymerization of amyloid-beta, human islet amyloid polypeptide (hIAPP, or also known as amylin) and alpha-synuclein. SEVI (semen-derived enhancer of viral infection) amyloid formation by the cross-seeding between the bacterial curli protein and PAP248-286 is also briefly discussed.
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Affiliation(s)
- Magdalena I Ivanova
- Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk 28119, South Korea; Bio-Analytical Science, University of Science and Technology, Daejeon 34113, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, South Korea; Research headquarters, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Ohio, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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63
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Zhang Y, Tang Y, Zhang D, Liu Y, He J, Chang Y, Zheng J. Amyloid cross-seeding between Aβ and hIAPP in relation to the pathogenesis of Alzheimer and type 2 diabetes. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.09.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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64
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Jiang P, Gan M, Dickson DW. Apoptotic Neuron-Derived Histone Amyloid Fibrils Induce α-Synuclein Aggregation. Mol Neurobiol 2021; 58:867-876. [PMID: 33048264 PMCID: PMC7855663 DOI: 10.1007/s12035-020-02167-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/09/2020] [Indexed: 10/23/2022]
Abstract
Cell-to-cell transfer of α-synuclein (αS) is increasingly thought to play an important role in propagation of αS pathology, but mechanisms responsible for formation of initial αS seeds and factors facilitating their propagation remain unclear. We previously demonstrated that αS aggregates are formed rapidly in apoptotic neurons and that interaction between cytoplasmic αS and proaggregant nuclear factors generates seed-competent αS. We also provided initial evidence that histones have proaggregant properties. Since histones are released from cells undergoing apoptosis or cell stress, we hypothesized that internalization of histones into αS expressing cells could lead to intracellular αS aggregation. Here using mCherry-tagged histone, we show that nuclear extracts from apoptotic cells can induce intracellular αS inclusions after uptake into susceptible cells, while extracts from non-apoptotic cells did not. We also demonstrate that nuclear extracts from apoptotic cells contained histone-immunoreactive amyloid fibrils. Moreover, recombinant histone-derived amyloid fibrils are able to induce αS aggregation in cellular and animal models. Induction of αS aggregation by histone amyloid fibrils is associated with endocytosis-mediated rupture of lysosomes, and this effect can be enhanced in cells with chemically induced lysosomal membrane defects. These studies provide initial descriptions of the contribution of histone amyloid fibrils to αS aggregation.
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Affiliation(s)
- Peizhou Jiang
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
| | - Ming Gan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA.
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65
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Rodríguez Gama A, Miller T, Halfmann R. Mechanics of a molecular mousetrap-nucleation-limited innate immune signaling. Biophys J 2021; 120:1150-1160. [PMID: 33460595 PMCID: PMC8059202 DOI: 10.1016/j.bpj.2021.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/17/2022] Open
Abstract
Innate immune responses, such as cell death and inflammatory signaling, are typically switch-like in nature. They also involve "prion-like" self-templating polymerization of one or more signaling proteins into massive macromolecular assemblies known as signalosomes. Despite the wealth of atomic-resolution structural information on signalosomes, how the constituent polymers nucleate and whether the switch-like nature of that event at the molecular scale relates to the digital nature of innate immune signaling at the cellular scale remains unknown. In this perspective, we review current knowledge of innate immune signalosome assembly, with an emphasis on structural constraints that allow the proteins to accumulate in inactive soluble forms poised for abrupt polymerization. We propose that structurally encoded nucleation barriers to protein polymerization kinetically regulate the corresponding pathways, which allows for extremely sensitive, rapid, and decisive signaling upon pathogen detection. We discuss how nucleation barriers satisfy the rigorous on-demand functions of the innate immune system but also predispose the system to precocious activation that may contribute to progressive age-associated inflammation.
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Affiliation(s)
| | - Tayla Miller
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, Missouri; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas.
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66
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Zottig X, Al-Halifa S, Côté-Cyr M, Calzas C, Le Goffic R, Chevalier C, Archambault D, Bourgault S. Self-assembled peptide nanorod vaccine confers protection against influenza A virus. Biomaterials 2021; 269:120672. [PMID: 33476893 DOI: 10.1016/j.biomaterials.2021.120672] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 12/23/2022]
Abstract
Proteinaceous nanostructures have emerged as a promising strategy to develop safe and efficient subunit vaccines. The ability of synthetic β-sheet self-assembling peptides to stabilize antigenic determinants and to potentiate the epitope-specific immune responses have highlighted their potential as an immunostimulating platform for antigen delivery. Nonetheless, the intrinsic polymorphism of the resulting cross-β fibrils, their length in the microscale and their close structural similarity with pathological amyloids could limit their usage in vaccinology. In this study, we harnessed electrostatic capping motifs to control the self-assembly of a chimeric peptide comprising a 10-mer β-sheet sequence and a highly conserved epitope derived from the influenza A virus (M2e). Self-assembly led to the formation of 100-200 nm long uniform nanorods (NRs) displaying the M2e epitope on their surface. These cross-β assemblies differed from prototypical amyloid fibrils owing to low polydispersity, short length, non-binding to thioflavin T and Congo Red dyes, and incapacity to seed homologous amyloid assembly. M2e-NRs were efficiently uptaken by antigen presenting cells and the cross-β quaternary architecture activated the Toll-like receptor 2 and stimulated dendritic cells. Mice subcutaneous immunization revealed a robust M2e-specific IgG response, which was dependent on self-assembly into NRs. Upon intranasal immunization in combination with the polymeric adjuvant montanide gel, M2e-NRs conferred complete protection with absence of clinical signs against a lethal experimental infection with the H1N1 influenza A virus. These findings indicate that by acting as an immunostimulator and delivery system, synthetic peptide-based NRs constitute a versatile self-adjuvanted nanoplatform for the delivery of subunit vaccines.
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Affiliation(s)
- Ximena Zottig
- Chemistry Department, Université du Québec à Montréal, Montreal, Canada; Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Quebec, Canada; Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada; The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Sainte-Hyacinthe, Canada
| | - Soultan Al-Halifa
- Chemistry Department, Université du Québec à Montréal, Montreal, Canada; Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Quebec, Canada; Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada; The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Sainte-Hyacinthe, Canada
| | - Mélanie Côté-Cyr
- Chemistry Department, Université du Québec à Montréal, Montreal, Canada; Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Quebec, Canada; Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada; The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Sainte-Hyacinthe, Canada
| | - Cynthia Calzas
- UR892 VIM, Equipe Virus Influenza, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Ronan Le Goffic
- UR892 VIM, Equipe Virus Influenza, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Christophe Chevalier
- UR892 VIM, Equipe Virus Influenza, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Denis Archambault
- Department of Biological Sciences, Université du Québec à Montréal, Montreal, Canada; The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Sainte-Hyacinthe, Canada.
| | - Steve Bourgault
- Chemistry Department, Université du Québec à Montréal, Montreal, Canada; Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Quebec, Canada; The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Sainte-Hyacinthe, Canada.
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67
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Multifunctional Amyloids in the Biology of Gram-Positive Bacteria. Microorganisms 2020; 8:microorganisms8122020. [PMID: 33348645 PMCID: PMC7766987 DOI: 10.3390/microorganisms8122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/18/2023] Open
Abstract
Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.
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68
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Yuzu K, Yamamoto N, Noji M, So M, Goto Y, Iwasaki T, Tsubaki M, Chatani E. Multistep Changes in Amyloid Structure Induced by Cross-Seeding on a Rugged Energy Landscape. Biophys J 2020; 120:284-295. [PMID: 33340544 DOI: 10.1016/j.bpj.2020.12.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/22/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022] Open
Abstract
Amyloid fibrils are aberrant protein aggregates associated with various amyloidoses and neurodegenerative diseases. It is recently indicated that structural diversity of amyloid fibrils often results in different pathological phenotypes, including cytotoxicity and infectivity. The diverse structures are predicted to propagate by seed-dependent growth, which is one of the characteristic properties of amyloid fibrils. However, much remains unknown regarding how exactly the amyloid structures are inherited to subsequent generations by seeding reaction. Here, we investigated the behaviors of self- and cross-seeding of amyloid fibrils of human and bovine insulin in terms of thioflavin T fluorescence, morphology, secondary structure, and iodine staining. Insulin amyloid fibrils exhibited different structures, depending on species, each of which replicated in self-seeding. In contrast, gradual structural changes were observed in cross-seeding, and a new type of amyloid structure with distinct morphology and cytotoxicity was formed when human insulin was seeded with bovine insulin seeds. Remarkably, iodine staining tracked changes in amyloid structure sensitively, and singular value decomposition analysis of the ultraviolet-visible absorption spectra of the fibril-bound iodine has revealed the presence of one or more intermediate metastable states during the structural changes. From these findings, we propose a propagation scheme with multistep structural changes in cross-seeding between two heterologous proteins, which is accounted for as a consequence of the rugged energy landscape of amyloid formation.
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Affiliation(s)
- Keisuke Yuzu
- Graduate School of Science, Kobe University, Kobe, Hyogo, Japan
| | - Naoki Yamamoto
- School of Medicine, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Masahiro Noji
- Institute for Protein Research, Osaka University, Suita, Osaka Japan; Graduate School of Human and Environmental Studies, Kyoto University, Yoshidanihonmatsu, Kyoto, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Suita, Osaka Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Suita, Osaka Japan; Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan
| | - Tetsushi Iwasaki
- Graduate School of Science, Kobe University, Kobe, Hyogo, Japan; Biosignal Research Center, Kobe University, Kobe, Hyogo, Japan
| | | | - Eri Chatani
- Graduate School of Science, Kobe University, Kobe, Hyogo, Japan.
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69
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Abstract
Self-assembly of proteins and peptides into the amyloid fold is a widespread phenomenon in the natural world. The structural hallmark of self-assembly into amyloid fibrillar assemblies is the cross-beta motif, which conveys distinct morphological and mechanical properties. The amyloid fibril formation has contrasting results depending on the organism, in the sense that it can bestow an organism with the advantages of mechanical strength and improved functionality or, on the contrary, could give rise to pathological states. In this chapter we review the existing information on amyloid-like peptide aggregates, which could either be derived from protein sequences, but also could be rationally or de novo designed in order to self-assemble into amyloid fibrils under physiological conditions. Moreover, the development of self-assembled fibrillar biomaterials that are tailored for the desired properties towards applications in biomedical or environmental areas is extensively analyzed. We also review computational studies predicting the amyloid propensity of the natural amino acid sequences and the structure of amyloids, as well as designing novel functional amyloid materials.
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Affiliation(s)
- C. Kokotidou
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
| | - P. Tamamis
- Texas A&M University, Artie McFerrin Department of Chemical Engineering College Station Texas 77843-3122 USA
| | - A. Mitraki
- University of Crete, Department of Materials Science and Technology Voutes Campus GR-70013 Heraklion Crete Greece
- FORTH, Institute for Electronic Structure and Laser N. Plastira 100 GR 70013 Heraklion Greece
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70
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Dec R, Dzwolak W. Extremely Amyloidogenic Single-Chain Analogues of Insulin's H-Fragment: Structural Adaptability of an Amyloid Stretch. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12150-12159. [PMID: 32988199 PMCID: PMC7586408 DOI: 10.1021/acs.langmuir.0c01747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Relatively short amino acid sequences often play a pivotal role in triggering protein aggregation leading to the formation of amyloid fibrils. In the case of insulin, various regions of A- and B-chains have been implicated as the most relevant to the protein's amyloidogenicity. Here, we focus on the highly amyloidogenic H-fragment of insulin comprising the disulfide-bonded N-terminal parts of both chains. Analysis of the aggregation behavior of single-chain peptide derivatives of the H-fragment suggests that the A-chain's part initiates the aggregation process while the disulfide-tethered B-chain reluctantly adapts to amyloid structure. Merging of both A- and B-parts into single-chain continuous peptides (A-B and B-A) results in extreme amyloidogenicity exceeding that of the double-chain H-fragment as reflected by almost instantaneous de novo fibrillization. Amyloid fibrils of A-B and B-A present distinct morphological and infrared traits and do not cross-seed insulin. Our study suggests that the N-terminal part of insulin's A-chain containing the intact Cys6-Cys11 intrachain disulfide bond may constitute insulin's major amyloid stretch which, through its bent conformation, enforces a parallel in-register alignment of β-strands. Comparison of the self-association behavior of H, A-B, and B-A peptides suggests that A-chain's N-terminal amyloid stretch is very versatile and adaptive to various structural contexts.
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71
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Heo CE, Han JY, Lim S, Lee J, Im D, Lee MJ, Kim YK, Kim HI. ATP Kinetically Modulates Pathogenic Tau Fibrillations. ACS Chem Neurosci 2020; 11:3144-3152. [PMID: 32915536 DOI: 10.1021/acschemneuro.0c00479] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advanced understanding of Alzheimer's disease (AD) and several tauopathies over the past decades indicates the pathological importance of tau aggregation in these diseases. Herein, we demonstrated that adenosine triphosphate (ATP), a highly charged anionic molecule found abundantly in the cytosol of cells, catalyzes fibrillation of tau as well as human islet amyloid polypeptide, a representative of basic intrinsically disordered proteins. Our results showed that ATP attracts multiple lysine residues of the four-repeat domain of tau (K18) via supramolecular complexation, thereby forming dimers that are converted to nuclei and accelerate fibril elongation. However, ATP was not directly incorporated into the K18 fibrils, suggesting that ATP plays the role of a catalyst, rather than a reactant, during K18 fibrillation. We also characterized the correlation between ATP dyshomeostasis and tau aggregation in the cellular environment. Our multiple biophysical approaches, including native mass spectrometry (MS), small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulation, provided insights into the molecular-level influence of ATP on the structural changes and fibrillation of tau.
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Affiliation(s)
- Chae Eun Heo
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center for Proteogenomics Research, Korea University, Seoul 02841, Republic of Korea
| | - Jong Yoon Han
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center for Proteogenomics Research, Korea University, Seoul 02841, Republic of Korea
| | - Sungsu Lim
- Brain Science Institute, Center for Neuromedicine, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Jeeyoung Lee
- Department of Biomedical Sciences, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Dongjoon Im
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center for Proteogenomics Research, Korea University, Seoul 02841, Republic of Korea
| | - Min Jae Lee
- Department of Biomedical Sciences, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Yun Kyung Kim
- Brain Science Institute, Center for Neuromedicine, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Biological Chemistry, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Hugh I. Kim
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Center for Proteogenomics Research, Korea University, Seoul 02841, Republic of Korea
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72
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Kaur A, Kaur A, Goyal D, Goyal B. How Does the Mono-Triazole Derivative Modulate Aβ 42 Aggregation and Disrupt a Protofibril Structure: Insights from Molecular Dynamics Simulations. ACS OMEGA 2020; 5:15606-15619. [PMID: 32637837 PMCID: PMC7331201 DOI: 10.1021/acsomega.0c01825] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/08/2020] [Indexed: 05/31/2023]
Abstract
Clinical studies have identified that abnormal self-assembly of amyloid-β (Aβ) peptide into toxic fibrillar aggregates is associated with the pathology of Alzheimer's disease (AD). The most acceptable therapeutic approach to stop the progression of AD is to inhibit the formation of β-sheet-rich structures. Recently, we designed and evaluated a series of novel mono-triazole derivatives 4(a-x), where compound 4v was identified as the most potent inhibitor of Aβ42 aggregation and disaggregates preformed Aβ42 fibrils significantly. Moreover, 4v strongly averts the Cu2+-induced Aβ42 aggregation and disaggregates the preformed Cu2+-induced Aβ42 fibrils, halts the generation of reactive oxygen species, and shows neuroprotective effects in SH-SY5Y cells. However, the underlying molecular mechanism of inhibition of Aβ42 aggregation by 4v and disaggregation of preformed Aβ42 fibrils remains obscure. In this work, molecular dynamics (MD) simulations have been performed to explore the conformational ensemble of the Aβ42 monomer and a pentameric protofibril structure of Aβ42 in the presence of 4v. The MD simulations highlighted that 4v binds preferentially at the central hydrophobic core region of the Aβ42 monomer and chains D and E of the Aβ42 protofibril. The dictionary of secondary structure of proteins analysis indicated that 4v retards the conformational conversion of the helix-rich structure of the Aβ42 monomer into the aggregation-prone β-sheet conformation. The binding free energy calculated by the molecular mechanics Poisson-Boltzmann surface area method revealed an energetically favorable process with ΔG binding = -44.9 ± 3.3 kcal/mol for the Aβ42 monomer-4v complex. The free energy landscape analysis highlighted that the Aβ42 monomer-4v complex sampled conformations with significantly higher helical contents (35 and 49%) as compared to the Aβ42 monomer alone (17%). Compound 4v displayed hydrogen bonding with Gly37 (chain E) and π-π interactions with Phe19 (chain D) of the Aβ42 protofibril. Further, the per-residue binding free energy analysis also highlighted that Phe19 (chain D) and Gly37 (chain E) of the Aβ42 protofibril showed the maximum contribution in the binding free energy. The decreased binding affinity and residue-residue contacts between chains D and E of the Aβ42 protofibril in the presence of 4v indicate destabilization of the Aβ42 protofibril structure. Overall, the structural information obtained through MD simulations indicated that 4v stabilizes the native helical conformation of the Aβ42 monomer and persuades a destabilization in the protofibril structure of Aβ42. The results of the study will be useful in the rational design of potent inhibitors against amyloid aggregation.
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Affiliation(s)
- Amandeep Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anupamjeet Kaur
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Bhupesh Goyal
- School
of Chemistry & Biochemistry, Thapar
Institute of Engineering & Technology, Patiala 147004, Punjab, India
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73
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Ciccone L, Shi C, di Lorenzo D, Van Baelen AC, Tonali N. The Positive Side of the Alzheimer's Disease Amyloid Cross-Interactions: The Case of the Aβ 1-42 Peptide with Tau, TTR, CysC, and ApoA1. Molecules 2020; 25:E2439. [PMID: 32456156 PMCID: PMC7288020 DOI: 10.3390/molecules25102439] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) represents a progressive amyloidogenic disorder whose advancement is widely recognized to be connected to amyloid-β peptides and Tau aggregation. However, several other processes likely contribute to the development of AD and some of them might be related to protein-protein interactions. Amyloid aggregates usually contain not only single type of amyloid protein, but also other type of proteins and this phenomenon can be rationally explained by the process of protein cross-seeding and co-assembly. Amyloid cross-interaction is ubiquitous in amyloid fibril formation and so a better knowledge of the amyloid interactome could help to further understand the mechanisms of amyloid related diseases. In this review, we discuss about the cross-interactions of amyloid-β peptides, and in particular Aβ1-42, with other amyloids, which have been presented either as integrated part of Aβ neurotoxicity process (such as Tau) or conversely with a preventive role in AD pathogenesis by directly binding to Aβ (such as transthyretin, cystatin C and apolipoprotein A1). Particularly, we will focus on all the possible therapeutic strategies aiming to rescue the Aβ toxicity by taking inspiration from these protein-protein interactions.
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Affiliation(s)
- Lidia Ciccone
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Chenghui Shi
- CNRS, BioCIS, Université Paris-Saclay, rue Jean-Baptiste Clément 5, 92290 Châtenay-Malabry, France; (C.S.); (D.d.L.)
| | - Davide di Lorenzo
- CNRS, BioCIS, Université Paris-Saclay, rue Jean-Baptiste Clément 5, 92290 Châtenay-Malabry, France; (C.S.); (D.d.L.)
| | - Anne-Cécile Van Baelen
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris Saclay, SIMoS, 91191 Gif-sur-Yvette, France;
| | - Nicolo Tonali
- CNRS, BioCIS, Université Paris-Saclay, rue Jean-Baptiste Clément 5, 92290 Châtenay-Malabry, France; (C.S.); (D.d.L.)
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74
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Tripathi T, Khan H. Direct Interaction between the β-Amyloid Core and Tau Facilitates Cross-Seeding: A Novel Target for Therapeutic Intervention. Biochemistry 2020; 59:341-342. [PMID: 31944100 DOI: 10.1021/acs.biochem.9b01087] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The deposition of amyloid-β (Aβ) plaques and tau-based neurofibrillary tangles is a neuropathological feature of Alzheimer's disease (AD). While studies have shown that the Aβ and tau interaction results in elevated AD pathology, the molecular linkage and mechanism of interaction of Aβ and tau are unclear. A recent study demonstrated the direct interaction between the Aβ core and specific regions of tau that facilitates pathological cross-seeding via a shared epitope. The data suggest that targeting the common epitope could be a more effective treatment strategy rather than targeting only Aβ or only tau. The findings have an important clinical significance for AD and related tauopathies.
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Affiliation(s)
- Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry , North-Eastern Hill University , Umshing, Shillong , Meghalaya 793022 , India
| | - Heena Khan
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry , North-Eastern Hill University , Umshing, Shillong , Meghalaya 793022 , India
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75
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Unsupervised Grammar Induction for Revealing the Internal Structure of Protein Sequence Motifs. Artif Intell Med 2020. [DOI: 10.1007/978-3-030-59137-3_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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76
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Werner T, Horvath I, Wittung-Stafshede P. Crosstalk Between Alpha-Synuclein and Other Human and Non-Human Amyloidogenic Proteins: Consequences for Amyloid Formation in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2020; 10:819-830. [PMID: 32538869 PMCID: PMC7458506 DOI: 10.3233/jpd-202085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/13/2020] [Indexed: 02/07/2023]
Abstract
It was recently shown (Sampson et al., Elife9, 2020) that an amyloidogenic protein, CsgA, present in E. coli biofilms in the gut can trigger Parkinson's disease in mice. This study emphasizes the possible role of the gut microbiome in modulation (and even initiation) of human neurodegenerative disorders, such as Parkinson's disease. As the CsgA protein was found to accelerate alpha-synuclein (the key amyloidogenic protein in Parkinson's disease) amyloid formation in vitro, this result suggests that also other amyloidogenic proteins from gut bacteria, and even from the diet (such as stable allergenic proteins), may be able to affect human protein conformations and thereby modulate amyloid-related diseases. In this review, we summarize what has been reported in terms of in vitro cross-reactivity studies between alpha-synuclein and other amyloidogenic human and non-human proteins. It becomes clear from the limited data that exist that there is a fine line between acceleration and inhibition, but that cross-reactivity is widespread, and it is more common for other proteins (among the studied cases) to accelerate alpha-synuclein amyloid formation than to block it. It is of high importance to expand investigations of cross-reactivity between amyloidogenic proteins to both reveal underlying mechanisms and links between human diseases, as well as to develop new treatments that may be based on an altered gut microbiome.
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Affiliation(s)
- Tony Werner
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Istvan Horvath
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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77
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Akbarian M, Kianpour M, Yousefi R, Moosavi-Movahedi AA. Characterization of insulin cross-seeding: the underlying mechanism reveals seeding and denaturant-induced insulin fibrillation proceeds through structurally similar intermediates. RSC Adv 2020; 10:29885-29899. [PMID: 35518209 PMCID: PMC9056291 DOI: 10.1039/d0ra05414c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/29/2020] [Indexed: 02/01/2023] Open
Abstract
Insulin rapidly fibrillates in the presence of amyloid seeds from different sources. To address its cross-reactivity we chose the seeds of seven model proteins and peptides along with the seeds of insulin itself. Model candidates were selected/designed according to their size, amino acid sequence, and hydrophobicity. We found while some seeds provided catalytic ends for inducing the formation of non-native insulin conformers and increase fibrillation, others attenuated insulin fibrillation kinetics. We also observed competition between the intermediate insulin conformers which formed with urea and amyloid seeds in entering the fibrillogenic pathway. Simultaneous incubation of insulin with urea and amyloid seeds resulted in the formation of nearly similar insulin intermediate conformers which synergistically enhance insulin fibrillation kinetics. Given these results, it is highly likely that, structurally, there is a specific intermediate in different pathways of insulin fibrillation that governs fibrillation kinetics and morphology of the final mature fibril. Overall, this study provides a novel mechanistic insight into insulin fibrillation and gives new information on how seeds of different proteins are capable of altering insulin fibrillation kinetics and morphology. This report, for the first time, tries to answer an important question that why fibrillation of insulin is either accelerated or attenuated in the presence of amyloid fibril seeds from different sources. Native insulins in the presence of low urea concentrations or seeds with low hydrophobicity form ordered aggregates (amyloid fibrils), while high urea concentrations or the seeds with high level of hydrophobicity can induce the amorphous aggregation.![]()
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Affiliation(s)
- Mohsen Akbarian
- Protein Chemistry Laboratory (PCL)
- Department of Biology
- College of Sciences
- Shiraz University
- Shiraz
| | - Maryam Kianpour
- Protein Chemistry Laboratory (PCL)
- Department of Biology
- College of Sciences
- Shiraz University
- Shiraz
| | - Reza Yousefi
- Protein Chemistry Laboratory (PCL)
- Department of Biology
- College of Sciences
- Shiraz University
- Shiraz
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O'Carroll A, Coyle J, Gambin Y. Prions and Prion-like assemblies in neurodegeneration and immunity: The emergence of universal mechanisms across health and disease. Semin Cell Dev Biol 2019; 99:115-130. [PMID: 31818518 DOI: 10.1016/j.semcdb.2019.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023]
Abstract
Prion-like behaviour is an abrupt process, an "all-or-nothing" transition between a monomeric species and an "infinite" fibrillated form. Once a nucleation point is formed, the process is unstoppable as fibrils self-propagate by recruiting and converting all monomers into the amyloid fold. After the "mad cow" episode, prion diseases have made the headlines, but more and more prion-like behaviours have emerged in neurodegenerative diseases, where formation of fibrils and large conglomerates of proteins deeply disrupt the cell homeostasis. More interestingly, in the last decade, examples emerged to suggest that prion-like conversion can be used as a positive gain of function, for memory storage or structural scaffolding. More recent experiments show that we are only seeing the tip of the iceberg and that, for example, prion-like amplification is found in many pathways of the immune response. In innate immunity, receptors on the cellular surface or within the cells 'sense' danger and propagate this information as signal, through protein-protein interactions (PPIs) between 'receptor', 'adaptor' and 'effector' proteins. In innate immunity, the smallest signal of a foreign element or pathogen needs to trigger a macroscopic signal output, and it was found that adaptor polymerize to create an extreme signal amplification. Interestingly, our body uses multiple structural motifs to create large signalling platform; a few innate proteins use amyloid scaffolds but most of the polymers discovered are composed by self-assembly in helical filaments. Some of these helical assemblies even have intercellular "contamination" in a "true" prion action, as demonstrated for ASC specks and MyD88 filaments. Here, we will describe the current knowledge in neurodegenerative diseases and innate immunity and show how these two very different fields can cross-seed discoveries.
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Affiliation(s)
- Ailis O'Carroll
- EMBL Australia Node in Single Molecule Sciences, and School of Medical Sciences, Faculty of Edicine, The University of New South Wales, Sydney, Australia
| | - Joanne Coyle
- EMBL Australia Node in Single Molecule Sciences, and School of Medical Sciences, Faculty of Edicine, The University of New South Wales, Sydney, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Sciences, and School of Medical Sciences, Faculty of Edicine, The University of New South Wales, Sydney, Australia.
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