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Kihal N, Archambault MJ, Babych M, Nazemi A, Bourgault S. Probing the molecular determinants of the activation of toll-like receptor 2/6 by amyloid nanostructures through directed peptide self-assembly. SOFT MATTER 2024. [PMID: 39225438 DOI: 10.1039/d4sm00638k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Amyloid fibrils are proteinaceous nanostructures known for their ability to activate the innate immune system, which has been recently exploited for their use as self-adjuvanted antigen delivery systems for vaccines. Among mechanisms of immunostimulation, the activation of the heterodimeric toll-like receptor 2/6 (TLR2/TLR6) by the cross-β-sheet quaternary conformation appears important. Nonetheless, the lack of control over the process of self-assembly and the polydispersity of the resulting supramolecular architectures make it challenging to elucidate the molecular basis of TLR2/TLR6 engagement by amyloid assemblies. In this context, we harnessed the effects of N- and C-terminal modifications of a short 10-mer β-peptide derived from the islet amyloid polypeptide (I10) to investigate the relationships between the morphology and physicochemical properties of amyloid assemblies and their TLR2/TLR6 activity. Chemical substitutions at the N- and C-termini of the I10 peptide, including addition of charged residues at the N-terminus and α-amidation of C-terminus, allowed the controlled formation of a diversity of architectures, including belt-like filaments, rigid nanorods as well as flat and twisted fibrils. These fully cytocompatible peptide nanostructures showed different potencies to activate TLR2/TLR6, which correlated with the charge exposed on the surface. These results further demonstrate the potent modulatory effect of N- and C-terminal electrostatic capping on the self-assembly of short synthetic β-peptides. This study also indicates that self-assembly into cross-β-sheet nanostructures is essential for the activation of the TLR2/TLR6 by amyloidogenic peptides, albeit the structural requirements of the engagement of this promiscuous immune receptor by the nanostructures remain challenging to precisely untangle.
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Affiliation(s)
- Nadjib Kihal
- Department of Chemistry, Université du Québec à Montréal. C.P.8888, Succursale Centre-Ville, Montréal, H3C 3P8, Canada.
- Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec, Canada
- Quebec Centre for Advanced Materials, QCAM, Montreal, Canada
| | - Marie-Jeanne Archambault
- Department of Chemistry, Université du Québec à Montréal. C.P.8888, Succursale Centre-Ville, Montréal, H3C 3P8, Canada.
- Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec, Canada
| | - Margaryta Babych
- Department of Chemistry, Université du Québec à Montréal. C.P.8888, Succursale Centre-Ville, Montréal, H3C 3P8, Canada.
- Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec, Canada
| | - Ali Nazemi
- Department of Chemistry, Université du Québec à Montréal. C.P.8888, Succursale Centre-Ville, Montréal, H3C 3P8, Canada.
- Quebec Centre for Advanced Materials, QCAM, Montreal, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal. C.P.8888, Succursale Centre-Ville, Montréal, H3C 3P8, Canada.
- Quebec Network for Research on Protein Function, Engineering and Applications (PROTEO), Québec, Canada
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2
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Behbahanipour M, Navarro S, Bárcenas O, Garcia-Pardo J, Ventura S. Bioengineered self-assembled nanofibrils for high-affinity SARS-CoV-2 capture and neutralization. J Colloid Interface Sci 2024; 674:753-765. [PMID: 38955007 DOI: 10.1016/j.jcis.2024.06.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/10/2024] [Accepted: 06/23/2024] [Indexed: 07/04/2024]
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spurred intense research efforts to develop new materials with antiviral activity. In this study, we genetically engineered amyloid-based nanofibrils for capturing and neutralizing SARS-CoV-2. Building upon the amyloid properties of a short Sup35 yeast prion sequence, we fused it to SARS-CoV-2 receptor-binding domain (RBD) capturing proteins, LCB1 and LCB3. By tuning the reaction conditions, we achieved the spontaneous self-assembly of the Sup35-LCB1 fusion protein into a highly homogeneous and well-dispersed amyloid-like fibrillar material. These nanofibrils exhibited high affinity for the SARS-CoV-2 RBD, effectively inhibiting its interaction with the angiotensin-converting enzyme 2 (ACE2) receptor, the primary entry point for the virus into host cells. We further demonstrate that this functional nanomaterial entraps and neutralizes SARS-CoV-2 virus-like particles (VLPs), with a potency comparable to that of therapeutic antibodies. As a proof of concept, we successfully fabricated patterned surfaces that selectively capture SARS-CoV-2 RBD protein on wet environments. Collectively, these findings suggest that these protein-only nanofibrils hold promise as disinfecting coatings endowed with selective SARS-CoV-2 neutralizing properties to combat viral spread or in the development of sensitive viral sampling and diagnostic tools.
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Affiliation(s)
- Molood Behbahanipour
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
| | - Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
| | - Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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3
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Avni A, Joshi A, Mukhopadhyay S. Hydrogen-Deuterium Exchange Vibrational Raman Spectroscopy Distinguishes Distinct Amyloid Polymorphs Comprising Altered Core Architecture. J Phys Chem Lett 2023:5592-5601. [PMID: 37307286 DOI: 10.1021/acs.jpclett.3c01086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibrils are ordered protein aggregates comprising a hydrogen-bonded central cross-β core displaying a structural diversity in their supramolecular packing arrangements within the core. Such an altered packing results in amyloid polymorphism that gives rise to morphological and biological strain diversities. Here, we show that vibrational Raman spectroscopy coupled with hydrogen/deuterium (H/D) exchange discerns the key structural features that are responsible for yielding diverse amyloid polymorphs. Such a noninvasive and label-free methodology allows us to structurally distinguish distinct amyloid polymorphs displaying altered hydrogen bonding and supramolecular packing within the cross-β structural motif. By using quantitative molecular fingerprinting and multivariate statistical analysis, we analyze key Raman bands for the protein backbone and side chains that allow us to capture the conformational heterogeneity and structural distributions within distinct amyloid polymorphs. Our results delineate the key molecular factors governing the structural diversity in amyloid polymorphs and can potentially simplify studying amyloid remodeling by small molecules.
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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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Meier BH, Böckmann A. Solid-State NMR Structure of Amyloid-β Fibrils. Methods Mol Biol 2023; 2551:53-62. [PMID: 36310196 DOI: 10.1007/978-1-0716-2597-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Amyloid fibrils are involved in a number of diseases and notably play a role in neurodegeneration, where they are present in plaques in the brain. Their structure determination might help in finding ways to interfere with their formation, and ultimately prevent disease, by revealing the structure-function relationship and helping to design molecules targeting initial assembly steps and further propagation. Here, we describe the different steps in NMR protocols which allowed the 3D structure determination of amyloid-β fibrils.
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Affiliation(s)
- Beat H Meier
- Physical Chemistry, ETH Zurich, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, Lyon, France.
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6
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Jayawardena BM, Peacey L, Gamsjaeger R, Jones CE. Essential Role of Histidine for Rapid Copper(II)-Mediated Disassembly of Neurokinin B Amyloid. Biomolecules 2022; 12:biom12111585. [PMID: 36358935 PMCID: PMC9687585 DOI: 10.3390/biom12111585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 12/02/2022] Open
Abstract
Neurokinin B is a tachykinin peptide involved in a diverse range of neuronal functions. It rapidly forms an amyloid, which is considered physiologically important for efficient packing into dense core secretory vesicles within hypothalamic neurons. Disassembly of the amyloid is thought to require the presence of copper ions, which interact with histidine at the third position in the peptide sequence. However, it is unclear how the histidine is involved in the amyloid structure and why copper coordination can trigger disassembly. In this work, we demonstrate that histidine contributes to the amyloid structure via π-stacking interactions with nearby phenylalanine residues. The ability of neurokinin B to form an amyloid is dependent on any aromatic residue at the third position in the sequence; however, only the presence of histidine leads to both amyloid formation and rapid copper-induced disassembly.
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7
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Mehra S, Ahlawat S, Kumar H, Datta D, Navalkar A, Singh N, Patel K, Gadhe L, Kadu P, Kumar R, Jha NN, Sakunthala A, Sawner AS, Padinhateeri R, Udgaonkar JB, Agarwal V, Maji SK. α-Synuclein aggregation intermediates form fibril polymorphs with distinct prion-like properties. J Mol Biol 2022; 434:167761. [PMID: 35907572 DOI: 10.1016/j.jmb.2022.167761] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022]
Abstract
α-Synuclein (α-Syn) amyloids in synucleinopathies are suggested to be structurally and functionally diverse, reminiscent of prion-like strains. But how the aggregation of the same precursor protein results in the formation of fibril polymorphs remains elusive. Here, we demonstrate the structure-function relationship of two polymorphs, pre-matured fibrils (PMFs) and helix-matured fibrils (HMFs), based on α-Syn aggregation intermediates. These polymorphs display the structural differences as demonstrated by solid-state NMR and mass spectrometry studies and also possess different cellular activities such as seeding, internalization, and cell-to-cell transfer of aggregates. HMFs with a compact core structure exhibit low seeding potency but readily internalize and transfer from one cell to another. The less structured PMFs lack transcellular transfer ability but induce abundant α-Syn pathology and trigger the formation of aggresomes in cells. Overall, the study highlights that the conformational heterogeneity in the aggregation pathway may lead to fibril polymorphs with distinct prion-like behavior.
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Affiliation(s)
- Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Sahil Ahlawat
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad-500 046, India
| | - Harish Kumar
- Indian Institute of Science Education and Research, Pune- 411 008, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Nitu Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Rakesh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Narendra N Jha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Arunima Sakunthala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Ajay S Sawner
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research, Pune- 411 008, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad-500 046, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India.
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8
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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9
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Lau CYJ, Benne N, Lou B, Braake DT, Bosman E, van Kronenburg N, Fens M, Broere F, Hennink WE, Mastrobattista E. Tuning surface charges of peptide nanofibers for induction of antigen-specific immune tolerance: an introductory study. J Pharm Sci 2022; 111:1004-1011. [PMID: 35120963 DOI: 10.1016/j.xphs.2022.01.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022]
Abstract
Induction of antigen-specific immune tolerance has emerged as the next frontier in treating autoimmune disorders, including atherosclerosis and graft-vs-host reactions during transplantation. Nanostructures are under investigation as a platform for the coordinated delivery of critical components, i.e., the antigen epitope combined with tolerogenic agents, to the target immune cells and subsequently induce tolerance. In the present study, the utility of supramolecular peptide nanofibers to induce antigen-specific immune tolerance was explored. To study the influence of surface charges of the nanofibers towards the extent of the induced immune response, the flanking charge residues at both ends of the amphipathic fibrillization peptide sequences were varied. Dexamethasone, an immunosuppressive glucocorticoid drug, and the ovalbumin-derived OVA323-339 peptide that binds to I-A(d) MHC Class II were covalently linked at either end of the peptide sequences. It was shown that the functional extensions did not alter the structural integrity of the supramolecular nanofibers. Furthermore, the surface charges of the nanofibers were modulated by the inclusion of charged residues. Dendritic cell culture assays suggested that nanofiber of less negative ζ-potential can augment the antigen-specific tolerogenic response. Our findings illustrate a molecular approach to calibrate the tolerogenic response induced by peptide nanofibers, which pave the way for better design of future tolerogenic immunotherapies.
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Affiliation(s)
- Chun Yin Jerry Lau
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Naomi Benne
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Bo Lou
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands; Cardiovascular Research Institute, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, #08-01, MD6 Centre for Translational Medicine, 14 Medical Drive, 117599, Singapore
| | - Daniëlle Ter Braake
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Esmeralda Bosman
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Nicky van Kronenburg
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Marcel Fens
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Femke Broere
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Wim E Hennink
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Enrico Mastrobattista
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands.
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10
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Willbold D, Strodel B, Schröder GF, Hoyer W, Heise H. Amyloid-type Protein Aggregation and Prion-like Properties of Amyloids. Chem Rev 2021; 121:8285-8307. [PMID: 34137605 DOI: 10.1021/acs.chemrev.1c00196] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review will focus on the process of amyloid-type protein aggregation. Amyloid fibrils are an important hallmark of protein misfolding diseases and therefore have been investigated for decades. Only recently, however, atomic or near-atomic resolution structures have been elucidated from various in vitro and ex vivo obtained fibrils. In parallel, the process of fibril formation has been studied in vitro under highly artificial but comparatively reproducible conditions. The review starts with a summary of what is known and speculated from artificial in vitro amyloid-type protein aggregation experiments. A partially hypothetic fibril selection model will be described that may be suitable to explain why amyloid fibrils look the way they do, in particular, why at least all so far reported high resolution cryo-electron microscopy obtained fibril structures are in register, parallel, cross-β-sheet fibrils that mostly consist of two protofilaments twisted around each other. An intrinsic feature of the model is the prion-like nature of all amyloid assemblies. Transferring the model from the in vitro point of view to the in vivo situation is not straightforward, highly hypothetic, and leaves many open questions that need to be addressed in the future.
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Affiliation(s)
- Dieter Willbold
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.,Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
| | - Birgit Strodel
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Henrike Heise
- Institute of Biological Information Processing, Structural Biochemistry, IBI-7, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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11
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Grelich-Mucha M, Garcia AM, Torbeev V, Ożga K, Berlicki Ł, Olesiak-Bańska J. Autofluorescence of Amyloids Determined by Enantiomeric Composition of Peptides. J Phys Chem B 2021; 125:5502-5510. [PMID: 34008978 PMCID: PMC8182742 DOI: 10.1021/acs.jpcb.1c00808] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Amyloid fibrils are
peptide or protein aggregates possessing a
cross-β-sheet structure. They possess intrinsic fluorescence
property, which is still not fully understood. Herein, we compare
structural and optical properties of fibrils formed from L- and D-enantiomers
of the (105–115) fragment of transthyretin (TTR) and from their
racemic mixture. Our results show that autofluorescence of fibrils
obtained from enantiomers differs from that of fibrils from the racemic
mixture. In order to elucidate the origin of observed differences,
we analyzed the structure and morphology of fibrils and showed how
variations in β-sheet organization influence optical properties
of fibrils. We clarified the contribution of aromatic rings and the
amyloid backbone to the final blue-green emission of fibrils. This
work demonstrates how enantiomeric composition of amino acids allows
us to modulate the self-assembly and final morphology of well-defined
fibrillar bionanostructures with optical properties controlled by
supramolecular organization.
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Affiliation(s)
- Manuela Grelich-Mucha
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ana M Garcia
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, France
| | - Vladimir Torbeev
- Institute de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006) Strasbourg 67000, France
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Olesiak-Bańska
- Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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12
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Korang-Yeboah M, Ketcham S, Shih M, Ako-Adounvo AM, Zhang J, Bandaranayake BM, Abbey-Berko Y, Faustino P, Ashraf M. Effect of formulation and peptide folding on the fibrillar aggregation, gelation, and oxidation of a therapeutic peptide. Int J Pharm 2021; 604:120677. [PMID: 33961953 DOI: 10.1016/j.ijpharm.2021.120677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 11/28/2022]
Abstract
The physical and chemical stability of therapeutic peptides presents challenges in developing robust formulations. The stability of the formulation affects product safety, efficacy and quality. Therefore, an understanding of the effects of formulation variables on the peptide's conformational structure and on its possible physical and chemical degradation is vital. To this end, computational and experimental analysis were employed to investigate the impact of formulation, peptide folding and product handling on oxidation, fibrillar aggregation and gelation of teriparatide. Teriparatide was used as a model drug due to the correlation of its conformation in solution with its pharmacological activity. Fibrillar aggregation and gelation were monitored using four orthogonal techniques. An innovative, automated platform coupled with ion mobility mass spectrometry was used for profiling chemical degradants. Increases in teriparatide concentration, pH, and ionic strength were found to increase the rate of fibrillar aggregation and gelation. Conversely, an increase in peptide folding and stabilization of the folded structures was found to decrease the rate of fibrillar aggregation and gelation. Moreover, the rate of oxidation was found to be inversely related to its solution concentration and extent of peptide folding. The present study provides an insight into formulation strategies designed to reduce the potential risk of physical and chemical degradation of peptides with a defined conformation.
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Affiliation(s)
- Maxwell Korang-Yeboah
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA.
| | - Stephanie Ketcham
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA
| | - Mack Shih
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA
| | - Ann-Marie Ako-Adounvo
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA
| | - Jinhui Zhang
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA.
| | - Bandaranayake M Bandaranayake
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA
| | - Yvonne Abbey-Berko
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA.
| | - Patrick Faustino
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA.
| | - Muhammad Ashraf
- Division of Product Quality Research, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administration, MD, USA
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13
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Antonschmidt L, Dervişoğlu R, Sant V, Tekwani Movellan K, Mey I, Riedel D, Steinem C, Becker S, Andreas LB, Griesinger C. Insights into the molecular mechanism of amyloid filament formation: Segmental folding of α-synuclein on lipid membranes. SCIENCE ADVANCES 2021; 7:7/20/eabg2174. [PMID: 33990334 PMCID: PMC8121418 DOI: 10.1126/sciadv.abg2174] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/25/2021] [Indexed: 05/15/2023]
Abstract
Recent advances in the structural biology of disease-relevant α-synuclein fibrils have revealed a variety of structures, yet little is known about the process of fibril aggregate formation. Characterization of intermediate species that form during aggregation is crucial; however, this has proven very challenging because of their transient nature, heterogeneity, and low population. Here, we investigate the aggregation of α-synuclein bound to negatively charged phospholipid small unilamellar vesicles. Through a combination of kinetic and structural studies, we identify key time points in the aggregation process that enable targeted isolation of prefibrillar and early fibrillar intermediates. By using solid-state nuclear magnetic resonance, we show the gradual buildup of structural features in an α-synuclein fibril filament, revealing a segmental folding process. We identify distinct membrane-binding domains in α-synuclein aggregates, and the combined data are used to present a comprehensive mechanism of the folding of α-synuclein on lipid membranes.
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Affiliation(s)
- Leif Antonschmidt
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Rıza Dervişoğlu
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vrinda Sant
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, CA, USA
| | - Kumar Tekwani Movellan
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ingo Mey
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Dietmar Riedel
- Laboratory of Electron Microscopy, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Göttingen, Germany
- Biomolecular Chemistry Group, Max-Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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14
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Zhou J, Venturelli L, Keiser L, Sekatskii SK, Gallaire F, Kasas S, Longo G, Knowles TPJ, Ruggeri FS, Dietler G. Environmental Control of Amyloid Polymorphism by Modulation of Hydrodynamic Stress. ACS NANO 2021; 15:944-953. [PMID: 33348981 DOI: 10.1021/acsnano.0c07570] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The phenomenon of amyloid polymorphism is a key feature of protein aggregation. Unravelling this phenomenon is of great significance for understanding the underlying molecular mechanisms associated with neurodegenerative diseases and for the development of amyloid-based functional biomaterials. However, the understanding of the molecular origins and the physicochemical factors modulating amyloid polymorphs remains challenging. Herein, we demonstrate an association between amyloid polymorphism and environmental stress in solution, induced by an air/water interface in motion. Our results reveal that low-stress environments produce heterogeneous amyloid polymorphs, including twisted, helical, and rod-like fibrils, whereas high-stress conditions generate only homogeneous rod-like fibrils. Moreover, high environmental stress converts twisted fibrils into rod-like fibrils both in-pathway and after the completion of mature amyloid formation. These results enrich our understanding of the environmental origin of polymorphism of pathological amyloids and shed light on the potential of environmentally controlled fabrication of homogeneous amyloid biomaterials for biotechnological applications.
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Affiliation(s)
- Jiangtao Zhou
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Leonardo Venturelli
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ludovic Keiser
- Laboratory of Fluid Mechanics and Instabilities, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sergey K Sekatskii
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - François Gallaire
- Laboratory of Fluid Mechanics and Instabilities, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sandor Kasas
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giovanni Longo
- Istituto di Struttura della Materia, CNR, Via del Fosso del Cavaliere 100, 00133, Roma, Italy
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Francesco S Ruggeri
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Laboratory of Physical Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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15
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Seuring C, Verasdonck J, Gath J, Ghosh D, Nespovitaya N, Wälti MA, Maji SK, Cadalbert R, Güntert P, Meier BH, Riek R. The three-dimensional structure of human β-endorphin amyloid fibrils. Nat Struct Mol Biol 2020; 27:1178-1184. [PMID: 33046908 DOI: 10.1038/s41594-020-00515-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022]
Abstract
In the pituitary gland, hormones are stored in a functional amyloid state within acidic secretory granules before they are released into the blood. To gain a detailed understanding of the structure-function relationship of amyloids in hormone secretion, the three-dimensional (3D) structure of the amyloid fibril of the human hormone β-endorphin was determined by solid-state NMR. We find that β-endorphin fibrils are in a β-solenoid conformation with a protonated glutamate residue in their fibrillar core. During exocytosis of the hormone amyloid the pH increases from acidic in the secretory granule to neutral level in the blood, thus it is suggested-and supported with mutagenesis data-that the pH change in the cellular milieu acts through the deprotonation of glutamate 8 to release the hormone from the amyloid. For amyloid disassembly in the blood, it is proposed that the pH change acts together with a buffer composition change and hormone dilution. In the pituitary gland, peptide hormones can be stored as amyloid fibrils within acidic secretory granules before release into the blood stream. Here, we use solid-state NMR to determine the 3D structure of the amyloid fiber formed by the human hormone β-endorphin. We find that β-endorphin fibrils are in a β-solenoid conformation that is generally reminiscent of other functional amyloids. In the β-endorphin amyloid, every layer of the β-solenoid is composed of a single peptide and protonated Glu8 is located in the fibrillar core. The secretory granule has an acidic pH but, on exocytosis, the β-endorphin fibril would encounter neutral pH conditions (pH 7.4) in the blood; this pH change would result in deprotonation of Glu8 to release the hormone peptide from the amyloid. Analyses of β-endorphin variants carrying mutations in Glu8 support the role of the protonation state of this residue in fibril disassembly, among other environmental changes.
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Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Joeri Verasdonck
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Julia Gath
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Dhimam Ghosh
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| | | | | | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| | | | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.,Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland. .,Structural Biology Laboratory, The Salk Institute, La Jolla, CA, USA.
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16
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Hiramatsu T, Yamamoto N, Ha S, Masuda Y, Yasuda M, Ishigaki M, Yuzu K, Ozaki Y, Chatani E. Iodine staining as a useful probe for distinguishing insulin amyloid polymorphs. Sci Rep 2020; 10:16741. [PMID: 33028868 PMCID: PMC7542459 DOI: 10.1038/s41598-020-73460-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/27/2020] [Indexed: 01/26/2023] Open
Abstract
It is recently suggested that amyloid polymorphism, i.e., structural diversity of amyloid fibrils, has a deep relationship with pathology. However, its prompt recognition is almost halted due to insufficiency of analytical methods for detecting polymorphism of amyloid fibrils sensitively and quickly. Here, we propose that iodine staining, a historically known reaction that was firstly found by Virchow, can be used as a method for distinguishing amyloid polymorphs. When insulin fibrils were prepared and iodine-stained, they exhibited different colors depending on polymorphs. Each of the colors was inherited to daughter fibrils by seeding reactions. The colors were fundamentally represented as a sum of three absorption bands in visible region between 400 and 750 nm, and the bands showed different titration curves against iodine, suggesting that there are three specific iodine binding sites. The analysis of resonance Raman spectra and polarization microscope suggested that several polyiodide ions composed of I3− and/or I5− were formed on the grooves or the edges of β-sheets. It was concluded that the polyiodide species and conformations formed are sensitive to surface structure of amyloid fibrils, and the resultant differences in color will be useful for detecting polymorphism in a wide range of diagnostic samples.
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Affiliation(s)
- Takato Hiramatsu
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Naoki Yamamoto
- School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Seongmin Ha
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Yuki Masuda
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Mitsuru Yasuda
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Mika Ishigaki
- Raman Project Center for Medical and Biological Applications, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan.,Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan
| | - Keisuke Yuzu
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Yukihiro Ozaki
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan.,Molecular Photoscience Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Eri Chatani
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.
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17
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Kaur A, New EJ, Sunde M. Strategies for the Molecular Imaging of Amyloid and the Value of a Multimodal Approach. ACS Sens 2020; 5:2268-2282. [PMID: 32627533 DOI: 10.1021/acssensors.0c01101] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein aggregation has been widely implicated in neurodegenerative diseases such as Alzheimer's disease, frontotemporal dementia, Parkinson's disease, and Huntington disease, as well as in systemic amyloidoses and conditions associated with localized amyloid deposits, such as type-II diabetes. The pressing need for a better understanding of the factors governing protein assembly has driven research for the development of molecular sensors for amyloidogenic proteins. To date, a number of sensors have been developed that report on the presence of protein aggregates utilizing various modalities, and their utility demonstrated for imaging protein aggregation in vitro and in vivo. Analysis of these sensors highlights the various advantages and disadvantages of the different imaging modalities and makes clear that multimodal sensors with properties amenable to more than one imaging technique need to be developed. This critical review highlights the key molecular scaffolds reported for molecular imaging modalities such as fluorescence, positron emission tomography, single photon emission computed tomography, and magnetic resonance imaging and includes discussion of the advantages and disadvantages of each modality, and future directions for the design of amyloid sensors. We also discuss the recent efforts focused on the design and development of multimodal sensors and the value of cross-validation across multiple modalities.
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Affiliation(s)
- Amandeep Kaur
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, New South Wales 2006, Australia
- The University of Sydney, Nano Institute (Sydney Nano), The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Elizabeth J. New
- The University of Sydney, Nano Institute (Sydney Nano), The University of Sydney, Sydney, New South Wales 2006, Australia
- The University of Sydney, School of Chemistry, Faculty of Science, Sydney, New South Wales 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Margaret Sunde
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, New South Wales 2006, Australia
- The University of Sydney, Nano Institute (Sydney Nano), The University of Sydney, Sydney, New South Wales 2006, Australia
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18
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Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future. Chem Soc Rev 2020; 49:5473-5509. [PMID: 32632432 PMCID: PMC7445747 DOI: 10.1039/c9cs00199a] [Citation(s) in RCA: 304] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.
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Affiliation(s)
- Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, CB3 0HE, Cambridge, UK
| | - Hilal A. Lashuel
- Laboratory of Molecular Neurobiology and Neuroproteomics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ian W. Hamley
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Daniel Erik Otzen
- Department of Molecular Biology, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, Centre for Microbial Research, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David S. Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Raffaele Mezzenga
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
- Department of Materials, ETH Zurich, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
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19
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Exploration of Insulin Amyloid Polymorphism Using Raman Spectroscopy and Imaging. Biophys J 2020; 118:2997-3007. [PMID: 32428440 DOI: 10.1016/j.bpj.2020.04.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/10/2020] [Accepted: 04/27/2020] [Indexed: 11/20/2022] Open
Abstract
We aimed to investigate insulin amyloid fibril polymorphism caused by salt effects and heating temperature and to visualize the structural differences of the polymorphisms in situ using Raman imaging without labeling. The time course monitoring for amyloid formation was carried out in an acidic condition without any salts and with two species of salts (NaCl and Na2SO4) by heating at 60, 70, 80, and 90°C. The intensity ratio of two Raman bands at 1672 and 1657 cm-1 due to antiparallel β-sheet and α-helix structures, respectively, was revealed to be an indicator of amyloid fibril formation, and the relative proportion of the β-sheet structure was higher in the case with salts, especially at a higher temperature with Na2SO4. In conjunction with the secondary structural changes of proteins, the S-S stretching vibrational mode of a disulfide bond (∼514 cm-1) and the ratio of the tyrosine doublet I850/I826 were also found to be markers distinguishing polymorphisms of insulin amyloid fibrils by principal component analysis. Especially, amyloid fibrils with Na2SO4 media formed the gauche-gauche-gauche conformation of disulfide bond at a higher rate, but without any salts, the gauche-gauche-gauche conformation was partially transformed into the gauche-gauche-trans conformation at higher temperatures. The different environments of the hydroxyl groups of the tyrosine residue were assumed to be caused by fibril polymorphism. Raman imaging using these marker bands also successfully visualized the two- and three- dimensional structural differences of amyloid polymorphisms. These results demonstrate the potential of Raman imaging as a diagnostic tool for polymorphisms in tissues of amyloid-related diseases.
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20
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Lee HS, Lim YB. Slow-Motion Self-Assembly: Access to Intermediates with Heterochiral Peptides to Gain Control over Alignment Media Development. ACS NANO 2020; 14:3344-3352. [PMID: 32058708 DOI: 10.1021/acsnano.9b09070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Understanding the intermediates or transition states in organic reactions has made it possible to develop theories and to synthesize important compounds. In contrast to organic reaction intermediates and even protein folding intermediates, the intermediates of peptide/protein self-assembly are not very well understood. Here we report that the self-assembly kinetics of linear heterochiral peptides are significantly slower than those of the corresponding homochiral peptides, which enables direct microscopic observation of assembly intermediates. By designing racemic or asymmetric heterochiral peptides, we were able to discover unusual mixed helical (MP-helix) and overtwisted intermediates. The convergence of equilibrium morphology between the homochiral and heterochiral peptides enables us to reasonably deduce the unobservable intermediates of rapidly assembling homochiral peptides. By utilizing the discovered information about the assembly intermediates, we were able to develop a functional NMR alignment medium that enables the measurement of residual dipolar couplings (RDCs) in a time-dependent manner. Although much less studied than their cyclic counterparts, the linear form of heterochiral peptides provides a means of obtaining a more in-depth understanding of the self-assembly pathway and of developing sophisticated bottom-up materials.
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Affiliation(s)
- Hye-Soo Lee
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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21
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self‐Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional MaterialsIndian Institute of Science Education and Research (IISER) Kolkata Mohanpur, West Bengal 741246 India
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22
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Reja A, Afrose SP, Das D. Aldolase Cascade Facilitated by Self-Assembled Nanotubes from Short Peptide Amphiphiles. Angew Chem Int Ed Engl 2020; 59:4329-4334. [PMID: 31920004 DOI: 10.1002/anie.201914633] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Indexed: 12/25/2022]
Abstract
Early evolution benefited from a complex network of reactions involving multiple C-C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C-C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C-C bond cleavage and formation. This system shows morphology-dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen-bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.
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Affiliation(s)
- Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Syed Pavel Afrose
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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23
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Lin YC, Komatsu H, Ma J, Axelsen PH, Fakhraai Z. Identifying Polymorphs of Amyloid-β (1-40) Fibrils Using High-Resolution Atomic Force Microscopy. J Phys Chem B 2019; 123:10376-10383. [PMID: 31714085 DOI: 10.1021/acs.jpcb.9b07854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many amyloid-β fibril preparations are highly polymorphic, and the conditions under which they are formed determine their morphology. This report describes the application of high-resolution atomic force microscopy (HR-AFM), combined with volume-per-length analysis, to define, identify, and quantify the structural components of polymorphic Aβ fibril preparations. Volume-per-length analysis confirms that they are composed of discrete cross-β filaments, and the analysis of HR-AFM images yields the number of striations in each fibril. Compared to mass-per-length analysis by electron microscopy, HR-AFM analysis yields narrower distributions, facilitating rapid and label-free quantitative morphological characterization of Aβ fibril preparations.
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Affiliation(s)
| | - Hiroaki Komatsu
- Departments of Pharmacology, Biochemistry and Biophysics, and Medicine/Infectious Diseases , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104-6084 , United States
| | | | - Paul H Axelsen
- Departments of Pharmacology, Biochemistry and Biophysics, and Medicine/Infectious Diseases , University of Pennsylvania School of Medicine , Philadelphia , Pennsylvania 19104-6084 , United States
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24
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Eraña H, Charco JM, Di Bari MA, Díaz-Domínguez CM, López-Moreno R, Vidal E, González-Miranda E, Pérez-Castro MA, García-Martínez S, Bravo S, Fernández-Borges N, Geijo M, D’Agostino C, Garrido J, Bian J, König A, Uluca-Yazgi B, Sabate R, Khaychuk V, Vanni I, Telling GC, Heise H, Nonno R, Requena JR, Castilla J. Development of a new largely scalable in vitro prion propagation method for the production of infectious recombinant prions for high resolution structural studies. PLoS Pathog 2019; 15:e1008117. [PMID: 31644574 PMCID: PMC6827918 DOI: 10.1371/journal.ppat.1008117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/04/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
The resolution of the three-dimensional structure of infectious prions at the atomic level is pivotal to understand the pathobiology of Transmissible Spongiform Encephalopathies (TSE), but has been long hindered due to certain particularities of these proteinaceous pathogens. Difficulties related to their purification from brain homogenates of disease-affected animals were resolved almost a decade ago by the development of in vitro recombinant prion propagation systems giving rise to highly infectious recombinant prions. However, lack of knowledge about the molecular mechanisms of the misfolding event and the complexity of systems such as the Protein Misfolding Cyclic Amplification (PMCA), have limited generating the large amounts of homogeneous recombinant prion preparations required for high-resolution techniques such as solid state Nuclear Magnetic Resonance (ssNMR) imaging. Herein, we present a novel recombinant prion propagation system based on PMCA that substitutes sonication with shaking thereby allowing the production of unprecedented amounts of multi-labeled, infectious recombinant prions. The use of specific cofactors, such as dextran sulfate, limit the structural heterogeneity of the in vitro propagated prions and makes possible, for the first time, the generation of infectious and likely homogeneous samples in sufficient quantities for studies with high-resolution structural techniques as demonstrated by the preliminary ssNMR spectrum presented here. Overall, we consider that this new method named Protein Misfolding Shaking Amplification (PMSA), opens new avenues to finally elucidate the three-dimensional structure of infectious prions.
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Affiliation(s)
- Hasier Eraña
- CIC bioGUNE, Derio (Bizkaia), Spain
- ATLAS Molecular Pharma S. L. Derio (Bizkaia), Spain
| | | | - Michele A. Di Bari
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Enric Vidal
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain
| | | | | | | | - Susana Bravo
- Proteomics Lab, IDIS, Santiago de Compostela, Spain
| | | | - Mariví Geijo
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Claudia D’Agostino
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Joseba Garrido
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Jifeng Bian
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Anna König
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Boran Uluca-Yazgi
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Spain
| | - Vadim Khaychuk
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Ilaria Vanni
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Glenn C. Telling
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Henrike Heise
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Romolo Nonno
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Derio (Bizkaia), Spain
- IKERBasque, Basque Foundation for Science, Bilbao (Bizkaia), Spain
- * E-mail:
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25
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Marshall LR, Zozulia O, Lengyel-Zhand Z, Korendovych IV. Minimalist de novo Design of Protein Catalysts. ACS Catal 2019; 9:9265-9275. [PMID: 34094654 PMCID: PMC8174531 DOI: 10.1021/acscatal.9b02509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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26
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Li J, Pylypchuk I, Johansson DP, Kessler VG, Seisenbaeva GA, Langton M. Self-assembly of plant protein fibrils interacting with superparamagnetic iron oxide nanoparticles. Sci Rep 2019; 9:8939. [PMID: 31222107 PMCID: PMC6586877 DOI: 10.1038/s41598-019-45437-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 06/05/2019] [Indexed: 11/09/2022] Open
Abstract
In situ fibrillation of plant proteins in presence of the superparamagnetic iron oxide nanoparticles (NP) promoted formation of a hybrid nanocomposite. The morphology of NP-fibril composite was revealed using ex-situ atomic force microscopy (AFM) in air. The NP-fibrils were associated into extended multi-fibril structures, indicating that the addition of NPs promoted protein association via β-sheet assembly. Real-time movement of NPs attached to fibrils under an external magnetic field was visualized using in-situ AFM in liquid, revealing that composite structures were stable at low pH, and displaying dipolar property of the NPs in the composite at high pH. Changes in magnetic properties of NPs when interacting with protein fibrils were quantitatively mapped using magnetic force microscopy (MFM). The magnetic moment of the NPs in composite was increased by co-existing with protein at low pH, while their dipolar nature was maintained at high pH. Self-assembly of the protein into fibrils is accelerated with increasing NP concentration within an optimal range, which is attributed to a fibrillation-competent conformation of the peptides. The latter was explained by the formation of favorable hydrogen bonds, electrostatic interactions, and efficient surface energy transfer between NPs and proteins.
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Affiliation(s)
- Jing Li
- The Department of Molecular Sciences, SLU - Swedish University of Agricultural Sciences, Box 7015, SE-750 07, Uppsala, Sweden.
| | - Ievgen Pylypchuk
- The Department of Molecular Sciences, SLU - Swedish University of Agricultural Sciences, Box 7015, SE-750 07, Uppsala, Sweden
| | - Daniel P Johansson
- The Department of Molecular Sciences, SLU - Swedish University of Agricultural Sciences, Box 7015, SE-750 07, Uppsala, Sweden
| | - Vadim G Kessler
- The Department of Molecular Sciences, SLU - Swedish University of Agricultural Sciences, Box 7015, SE-750 07, Uppsala, Sweden
| | - Gulaim A Seisenbaeva
- The Department of Molecular Sciences, SLU - Swedish University of Agricultural Sciences, Box 7015, SE-750 07, Uppsala, Sweden.
| | - Maud Langton
- The Department of Molecular Sciences, SLU - Swedish University of Agricultural Sciences, Box 7015, SE-750 07, Uppsala, Sweden.
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27
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Matlahov I, van der Wel PC. Conformational studies of pathogenic expanded polyglutamine protein deposits from Huntington's disease. Exp Biol Med (Maywood) 2019; 244:1584-1595. [PMID: 31203656 PMCID: PMC6920524 DOI: 10.1177/1535370219856620] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Huntington’s disease, like other neurodegenerative diseases, continues to lack an
effective cure. Current treatments that address early symptoms ultimately fail
Huntington’s disease patients and their families, with the disease typically
being fatal within 10–15 years from onset. Huntington’s disease is an inherited
disorder with motor and mental impairment, and is associated with the genetic
expansion of a CAG codon repeat encoding a polyglutamine-segment-containing
protein called huntingtin. These Huntington’s disease mutations cause misfolding
and aggregation of fragments of the mutant huntingtin protein, thereby likely
contributing to disease toxicity through a combination of gain-of-toxic-function
for the misfolded aggregates and a loss of function from sequestration of
huntingtin and other proteins. As with other amyloid diseases, the mutant
protein forms non-native fibrillar structures, which in Huntington’s disease are
found within patients’ neurons. The intracellular deposits are associated with
dysregulation of vital processes, and inter-neuronal transport of aggregates may
contribute to disease progression. However, a molecular understanding of these
aggregates and their detrimental effects has been frustrated by insufficient
structural data on the misfolded protein state. In this review, we examine
recent developments in the structural biology of polyglutamine-expanded
huntingtin fragments, and especially the contributions enabled by advances in
solid-state nuclear magnetic resonance spectroscopy. We summarize and discuss
our current structural understanding of the huntingtin deposits and how this
information furthers our understanding of the misfolding mechanism and disease
toxicity mechanisms.
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Affiliation(s)
- Irina Matlahov
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Patrick Ca van der Wel
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
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28
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Chen M, Schafer NP, Wolynes PG. Surveying the Energy Landscapes of Aβ Fibril Polymorphism. J Phys Chem B 2018; 122:11414-11430. [PMID: 30215519 DOI: 10.1021/acs.jpcb.8b07364] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many unrelated proteins and peptides have been found spontaneously to form amyloid fibers above a critical concentration. Even for a single sequence, however, the amyloid fold is not a single well-defined structure. Although the cross-β hydrogen bonding pattern is common to all amyloids, all other aspects of amyloid fiber structures are sensitive to both the sequence of the aggregating peptides and the solvent conditions under which the aggregation occurs. Amyloid fibers are easy to identify and grossly characterize using microscopy, but their insolubility and aperiodicity along the dimensions transverse to the fiber axis have complicated detailed experimental structural characterization. In this paper, we explore the landscape of possibilities for amyloid protofilament structures that are made up of a single stack of peptides associated in a parallel in-register manner. We view this landscape as a two-dimensional version of the usual three-dimensional protein folding problem: the survey of the two-dimensional folds of protein ribbons. Adopting this view leads to a practical method of predicting stable protofilament structures of arbitrary sequences. We apply this scheme to variants of Aβ, the amyloid forming peptide that is characteristically associated with Alzheimer's disease. Consistent with what is known from experiment, we find that Aβ protofibrils are polymorphic. To our surprise, however, the ribbon-folding landscape of Aβ turned out to be strikingly simple. We confirm that, at the level of the monomeric protofilament, the landscape for the Aβ sequence is reasonably well funneled toward structures that are similar to those that have been determined by experiment. The landscape has more distinct minima than does a typical globular protein landscape but fewer and deeper minima than the landscape of a randomly shuffled sequence having the same overall composition. It is tempting to consider the possibility that the significant degree of funneling of Aβ's ribbon-folding landscape has arisen as a result of natural selection. More likely, however, the intermediate complexity of Aβ's ribbon-folding landscape has come from the post facto selection of the Aβ sequence as an object of study by researchers because only by having a landscape with some degree of funneling can ordered aggregation of such a peptide occur at in vivo concentrations. In addition to predicting polymorph structures, we show that predicted solubilities of polymorphs correlate with experiment and with their elongation free energies computed by coarse-grained molecular dynamics.
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Affiliation(s)
- Mingchen Chen
- Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.,Department of Bioengineering , Rice University , Houston , Texas 77005 , United States
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.,Department of Chemistry , Rice University , Houston , Texas 77005 , United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States.,Department of Chemistry , Rice University , Houston , Texas 77005 , United States
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29
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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: 46] [Impact Index Per Article: 7.7] [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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30
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Adamcik J, Mezzenga R. Amyloid Polymorphism in the Protein Folding and Aggregation Energy Landscape. Angew Chem Int Ed Engl 2018; 57:8370-8382. [DOI: 10.1002/anie.201713416] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Jozef Adamcik
- Department of Health Sciences & Technology ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
- Department of Materials ETH Zurich Wolfgang-Pauli-Strasse 10 8093 Zurich Switzerland
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31
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Adamcik J, Mezzenga R. Amyloid‐Polymorphie in der Energielandschaft der Faltung und Aggregation von Proteinen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713416] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jozef Adamcik
- Departement Gesundheitswissenschaften und Technologie ETH Zürich Schmelzbergstrasse 9 8092 Zürich Schweiz
| | - Raffaele Mezzenga
- Departement Gesundheitswissenschaften und Technologie ETH Zürich Schmelzbergstrasse 9 8092 Zürich Schweiz
- Departement Materialwissenschaft ETH Zürich Wolfgang-Pauli-Strasse 10 8093 Zürich Schweiz
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32
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Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene. Nat Commun 2018; 9:1836. [PMID: 29743480 PMCID: PMC5943278 DOI: 10.1038/s41467-018-04116-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/03/2018] [Indexed: 11/09/2022] Open
Abstract
Here we present a new approach to diffraction imaging of amyloid fibrils, combining a free-standing graphene support and single nanofocused X-ray pulses of femtosecond duration from an X-ray free-electron laser. Due to the very low background scattering from the graphene support and mutual alignment of filaments, diffraction from tobacco mosaic virus (TMV) filaments and amyloid protofibrils is obtained to 2.7 Å and 2.4 Å resolution in single diffraction patterns, respectively. Some TMV diffraction patterns exhibit asymmetry that indicates the presence of a limited number of axial rotations in the XFEL focus. Signal-to-noise levels from individual diffraction patterns are enhanced using computational alignment and merging, giving patterns that are superior to those obtainable from synchrotron radiation sources. We anticipate that our approach will be a starting point for further investigations into unsolved structures of filaments and other weakly scattering objects.
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33
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Vetri V, Piccirilli F, Krausser J, Buscarino G, Łapińska U, Vestergaard B, Zaccone A, Foderà V. Ethanol Controls the Self-Assembly and Mesoscopic Properties of Human Insulin Amyloid Spherulites. J Phys Chem B 2018; 122:3101-3112. [DOI: 10.1021/acs.jpcb.8b01779] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Valeria Vetri
- Dipartimento di Fisica e Chimica and Advanced Technologies Network Center (ATEN), Università degli Studi di Palermo, Viale delle Scienze ed.18, Palermo 90128, Italy
| | - Federica Piccirilli
- Dipartimento di Fisica e Chimica and Advanced Technologies Network Center (ATEN), Università degli Studi di Palermo, Viale delle Scienze ed.18, Palermo 90128, Italy
| | - Johannes Krausser
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, U.K
| | - Gianpiero Buscarino
- Dipartimento di Fisica e Chimica and Advanced Technologies Network Center (ATEN), Università degli Studi di Palermo, Viale delle Scienze ed.18, Palermo 90128, Italy
| | - Urszula Łapińska
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | | | - Alessio Zaccone
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA, U.K
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34
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Periole X, Huber T, Bonito-Oliva A, Aberg KC, van der Wel PCA, Sakmar TP, Marrink SJ. Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. J Phys Chem B 2018; 122:1081-1091. [PMID: 29254334 PMCID: PMC5857390 DOI: 10.1021/acs.jpcb.7b10233] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Amyloid fibrils are highly ordered protein aggregates associated with more than 40 human diseases. The exact conditions under which the fibrils are grown determine many types of reported fibril polymorphism, including different twist patterns. Twist-based polymorphs display unique mechanical properties in vitro, and the relevance of twist polymorphism in amyloid diseases has been suggested. We present transmission electron microscopy images of Aβ42-derived (amyloid β) fibrils, which are associated with Alzheimer's disease, demonstrating the presence of twist variability even within a single long fibril. To better understand the molecular underpinnings of twist polymorphism, we present a structural and thermodynamics analysis of molecular dynamics simulations of the twisting of β-sheet protofilaments of a well-characterized cross-β model: the GNNQQNY peptide from the yeast prion Sup35. The results show that a protofilament model of GNNQQNY is able to adopt twist angles from -11° on the left-hand side to +8° on the right-hand side in response to various external conditions, keeping an unchanged peptide structure. The potential of mean force (PMF) of this cross-β structure upon twisting revealed that only ∼2kBT per peptide are needed to stabilize a straight conformation with respect to the left-handed free-energy minimum. The PMF also shows that the canonical structural core of β-sheets, i.e., the hydrogen-bonded backbone β-strands, favors the straight conformation. However, the concerted effects of the side chains contribute to twisting, which provides a rationale to correlate polypeptide sequence, environmental growth conditions and number of protofilaments in a fibril with twist polymorphisms.
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Affiliation(s)
- Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Alessandra Bonito-Oliva
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Karina C Aberg
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Patrick C A van der Wel
- Department of Structural Biology and Center for Protein Conformational Diseases, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet , 141 57 Huddinge, Sweden
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
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35
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Lagarias P, Elkhou Y, Vedad J, Konstantinidi A, Profit AA, Kellici TF, Kolocouris A, Desamero RZB, Mavromoustakos T. Molecular Dynamics Simulations on the Bioactive Molecule of hIAPP22-29 (NFGAILSS) and Rational Drug Design. Methods Mol Biol 2018; 1824:1-16. [PMID: 30039398 DOI: 10.1007/978-1-4939-8630-9_1] [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: 06/08/2023]
Abstract
This chapter includes information about the structure in equilibrium of the bioactive molecule hIAPP22-29 (NFGAILSS). The experimental structure was derived using X-ray and its 2D NOESY NMR experiments in d 6-DMSO and d-HFIP solvents. This molecule contains eight of the ten amino acids of the 20-29 region of the human islet amyloid polypeptide (hIAPP) often referred as the "amyloidogenic core." Amyloid deposits are well-known to cause as many as 20 pathological neurodegenerative disorders such as Alzheimer, Parkinson, Huntington, and Creutzfeldt-Jakob. The experimental structure was relaxed using molecular dynamics (MD) in simulation boxes consisting in DMSO and HFIP; the latter not provided by the applied software. The calculations were performed in GPUs and supercomputers, and some basic scripting is described for reference. The simulations confirmed the inter- and intramolecular forces that led to an "amyloidogenic core" observed from NOE experiments. The results showed that in DMSO and HFIP environment, Phe is not in spatial proximity with Leu or Ile, and this is consistent with an amyloidogenic core. However, in an amphipathic environment such as the model lipid bilayers, this communication is possible and may influence peptide amyloidogenic properties. The knowledge gained through this study may contribute to the rational drug design of novel peptides or organic molecules acting by modifying preventing amyloidogenic properties of the hIAPP peptide.
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Affiliation(s)
- Panagiotis Lagarias
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Youness Elkhou
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Jayson Vedad
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Athina Konstantinidi
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Adam A Profit
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Tahsin F Kellici
- Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Antonios Kolocouris
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece
| | - Ruel Z B Desamero
- Department of Chemistry, York College and The Institute for Macromolecular Assemblies, Jamaica, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Thomas Mavromoustakos
- Division of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, Athens, Greece.
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Linser R. Solid-state NMR spectroscopic trends for supramolecular assemblies and protein aggregates. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:45-53. [PMID: 28869877 DOI: 10.1016/j.ssnmr.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR is able to generate structural data on sample preparations that are explicitly non-crystalline. In particular, for amyloid fibril samples, which can comprise significant degrees of sample disorder, solid-state NMR has been used very successfully. But also solid-state NMR studies of other supramolecular assemblies that have resisted assessment by more standard methods are being performed with increasing ease and biological impact, many of which are briefly reviewed here. New technical trends with respect to structure calculation, protein dynamics and smaller sample amounts have reshaped the field of solid-state NMR recently. In particular, proton-detected approaches based on fast Magic-Angle Spinning (MAS) were demonstrated for crystalline systems initially. Currently, such approaches are being expanded to the above-mentioned non-crystalline targets, the characterization of which can now be pursued with sample amounts on the order of a milligram. In this Trends article, I am giving a brief overview about achievements of the last years as well as the directions that the field has been heading into and delineate some satisfactory perspectives for solid-state NMR's future striving.
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Affiliation(s)
- Rasmus Linser
- Department Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
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Meier BH, Riek R, Böckmann A. Emerging Structural Understanding of Amyloid Fibrils by Solid-State NMR. Trends Biochem Sci 2017; 42:777-787. [PMID: 28916413 DOI: 10.1016/j.tibs.2017.08.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 11/28/2022]
Abstract
Amyloid structures at atomic resolution have remained elusive mainly because of their extensive polymorphism and because their polymeric properties have hampered structural studies by classical approaches. Progress in sample preparation, as well as solid-state NMR methods, recently enabled the determination of high-resolution 3D structures of fibrils such as the amyloid-β fibril, which is involved in Alzheimer's disease. Notably, the simultaneous but independent structure determination of Aβ1-42, a peptide that forms fibrillar deposits in the brain of Alzheimer patients, by two independent laboratories, which yielded virtually identical results, has highlighted how structures can be obtained that allow further functional investigation.
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Affiliation(s)
- Beat H Meier
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
| | - Roland Riek
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon,7 passage du Vercors, 69367 Lyon, France.
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