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Paul S, Gayen K, Cantavella PG, Escuder B, Singh N. Complex Pathways Drive Pluripotent Fmoc-Leucine Self-Assemblies. Angew Chem Int Ed Engl 2024:e202406220. [PMID: 38825832 DOI: 10.1002/anie.202406220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/04/2024]
Abstract
Nature uses complex self-assembly pathways to access distinct functional non-equilibrium self-assemblies. This remarkable ability to steer same set of biomolecules into different self-assembly states is done by avoiding thermodynamic pit. In synthetic systems, on demand control over 'Pathway Complexity' to access self-assemblies different from equilibrium structures remains challenging. Here we show versatile non-equilibrium assemblies of the same monomer via alternate assembly pathways. The assemblies nucleate using non-classical or classical nucleation routes into distinct metastable (transient hydrogels), kinetic (stable hydrogels) and thermodynamic structures [(poly)-crystals and 2D sheets]. Initial chemical and thermal inputs force the monomers to follow different assembly pathways and form soft-materials with distinct molecular arrangements than at equilibrium. In many cases, equilibrium structures act as thermodynamic sink which consume monomers from metastable structures giving transiently formed materials. This dynamics can be tuned chemically or thermally to slow down the dissolution of transient hydrogel, or skip the intermediate hydrogel altogether to reach final equilibrium assemblies. If required this metastable state can be kinetically trapped to give strong hydrogel stable over days. This method to control different self-assembly states can find potential use in similar biomimetic systems to access new materials for various applications.
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Affiliation(s)
- Subir Paul
- Institute of Advanced Materials, Universitat Jaume I, Avinguda de Vicent Sos Baynat, s/n, 12006, Castelló de la Plana, Castelló, Spain
| | - Kousik Gayen
- Institute of Advanced Materials, Universitat Jaume I, Avinguda de Vicent Sos Baynat, s/n, 12006, Castelló de la Plana, Castelló, Spain
| | - Pau Gil Cantavella
- Institute of Advanced Materials, Universitat Jaume I, Avinguda de Vicent Sos Baynat, s/n, 12006, Castelló de la Plana, Castelló, Spain
| | - Beatriu Escuder
- Institute of Advanced Materials, Universitat Jaume I, Avinguda de Vicent Sos Baynat, s/n, 12006, Castelló de la Plana, Castelló, Spain
| | - Nishant Singh
- Institute of Advanced Materials, Universitat Jaume I, Avinguda de Vicent Sos Baynat, s/n, 12006, Castelló de la Plana, Castelló, Spain
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2
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Xu C, Ou X, Wang B, Shen H, Liu J, Yang X, Zhou Q, Chau JHC, Sung HHY, Xing G, Lam JWY, Tang BZ. Modulation of Heterotypic and Homotypic Interactions to Visualize the Evolution of Organic Aggregates in a Fluorescence Turn-on Manner. J Am Chem Soc 2024; 146:4851-4863. [PMID: 38346857 DOI: 10.1021/jacs.3c13252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The abnormal evolution of membrane-less organelles into amyloid fibrils is a causative factor in many neurodegenerative diseases. Fundamental research on evolving organic aggregates is thus instructive for understanding the root causes of these diseases. In-situ monitoring of evolving molecular aggregates with built-in fluorescence properties is a reliable approach to reflect their subtle structural variation. To increase the sensitivity of real-time monitoring, we presented organic aggregates assembled by TPAN-2MeO, which is a triphenyl acrylonitrile derivative. TPAN-2MeO showed a morphological evolution with distinct turn-on emission. Upon rapid nanoaggregation, it formed non-emissive spherical aggregates in the kinetically metastable state. Experimental and simulation results revealed that the weak homotypic interactions between the TPAN-2MeO molecules liberated their molecular motion for efficient non-radiative decay, and the strong heterotypic interactions between TPAN-2MeO and water stabilized the molecular geometry favorable for the non-fluorescent state. After ultrasonication, the decreased heterotypic interactions and increased homotypic interactions acted synergistically to allow access to the emissive thermodynamic equilibrium state with a decent photoluminescence quantum yield (PLQY). The spherical aggregates were eventually transformed into micrometer-sized blocklike particles. Under mechanical stirring, the co-assembly of TPAN-2MeO and Pluronic F-127 formed uniform fluorescent platelets, inducing a significant enhancement in PLQY. These results decipher the stimuli-triggered structural variation of organic aggregates with concurrent sensitive fluorescence response and pave the way for a deep understanding of the evolutionary events of biogenic aggregates.
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Affiliation(s)
- Changhuo Xu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- MOE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, 999078, China
| | - Xinwen Ou
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Bingzhe Wang
- Institute of Applied Physics and Materials Engineering, University of Macau, Macau, 999078, China
| | - Hanchen Shen
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Junkai Liu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Xueqin Yang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Qingqing Zhou
- MOE Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, 999078, China
| | - Joe H C Chau
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Herman H Y Sung
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Guichuan Xing
- Institute of Applied Physics and Materials Engineering, University of Macau, Macau, 999078, China
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, China
- Center for Aggregation-Induced Emission, South China University of Technology, Guangzhou, 510640, China
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3
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Přáda Brichtová E, Krupová M, Bouř P, Lindo V, Gomes Dos Santos A, Jackson SE. Glucagon-like peptide 1 aggregates into low-molecular-weight oligomers off-pathway to fibrillation. Biophys J 2023; 122:2475-2488. [PMID: 37138517 PMCID: PMC10323027 DOI: 10.1016/j.bpj.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/04/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
The physical stability of peptide-based drugs is of great interest to the pharmaceutical industry. Glucagon-like peptide 1 (GLP-1) is a 31-amino acid peptide hormone, the analogs of which are frequently used in the treatment of type 2 diabetes. We investigated the physical stability of GLP-1 and its C-terminal amide derivative, GLP-1-Am, both of which aggregate into amyloid fibrils. While off-pathway oligomers have been proposed to explain the unusual aggregation kinetics observed previously for GLP-1 under specific conditions, these oligomers have not been studied in any detail. Such states are important as they may represent potential sources of cytotoxicity and immunogenicity. Here, we identified and isolated stable, low-molecular-weight oligomers of GLP-1 and GLP-1-Am, using size-exclusion chromatography. Under the conditions studied, isolated oligomers were shown to be resistant to fibrillation or dissociation. These oligomers contain between two and five polypeptide chains and they have a highly disordered structure as indicated by a variety of spectroscopic techniques. They are highly stable with respect to time, temperature, or agitation despite their noncovalent character, which was established using liquid chromatography-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results provide evidence of stable, low-molecular-weight oligomers that are formed by an off-pathway mechanism which competes with amyloid fibril formation.
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Affiliation(s)
- Eva Přáda Brichtová
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Monika Krupová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic; Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague 6, Czech Republic
| | - Viv Lindo
- AstraZeneca, Cambridge, United Kingdom
| | | | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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4
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Block AJ, Bartz JC. Prion strains: shining new light on old concepts. Cell Tissue Res 2023; 392:113-133. [PMID: 35796874 PMCID: PMC11318079 DOI: 10.1007/s00441-022-03665-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023]
Abstract
Prion diseases are a group of inevitably fatal neurodegenerative disorders affecting numerous mammalian species, including humans. The existence of heritable phenotypes of disease in the natural host suggested that prions exist as distinct strains. Transmission of sheep scrapie to rodent models accelerated prion research, resulting in the isolation and characterization of numerous strains with distinct characteristics. These strains are grouped into categories based on the incubation period of disease in different strains of mice and also by how stable the strain properties were upon serial passage. These classical studies defined the host and agent parameters that affected strain properties, and, prior to the advent of the prion hypothesis, strain properties were hypothesized to be the result of mutations in a nucleic acid genome of a conventional pathogen. The development of the prion hypothesis challenged the paradigm of infectious agents, and, initially, the existence of strains was difficult to reconcile with a protein-only agent. In the decades since, much evidence has revealed how a protein-only infectious agent can perform complex biological functions. The prevailing hypothesis is that strain-specific conformations of PrPSc encode prion strain diversity. This hypothesis can provide a mechanism to explain the observed strain-specific differences in incubation period of disease, biochemical properties of PrPSc, tissue tropism, and subcellular patterns of pathology. This hypothesis also explains how prion strains mutate, evolve, and adapt to new species. These concepts are applicable to prion-like diseases such as Parkinson's and Alzheimer's disease, where evidence of strain diversity is beginning to emerge.
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Affiliation(s)
- Alyssa J Block
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, 68178, USA
| | - Jason C Bartz
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, 68178, USA.
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5
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Pauly T, Zhang T, Sternke-Hoffmann R, Nagel-Steger L, Willbold D. Differentiation of subnucleus-sized oligomers and nucleation-competent assemblies of the Aβ peptide. Biophys J 2023; 122:269-278. [PMID: 36529991 PMCID: PMC9892607 DOI: 10.1016/j.bpj.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
A significant feature of Alzheimer's disease is the formation of amyloid deposits in the brain consisting mainly of misfolded derivatives of proteolytic cleavage products of the amyloid precursor protein amyloid-β (Aβ) peptide. While high-resolution structures already exist for both the monomer and the amyloid fibril of the Aβ peptide, the mechanism of amyloid formation itself still defies precise characterization. In this study, low and high molecular weight oligomers (LMWOs and HMWOs) were identified by sedimentation velocity analysis, and for the first time, the temporal evolution of oligomer size distributions was correlated with the kinetics of amyloid formation as determined by thioflavin T-binding studies. LMWOs of subnucleus size contain fewer than seven monomer units and exist alongside a heterogeneous group of HMWOs with 20-160 monomer units that represent potential centers of nucleus formation due to high local monomer concentrations. These HMWOs already have slightly increased β-strand content and appear structurally similar regardless of size, as shown by examination with a range of fluorescent dyes. Once fibril nuclei are formed, the monomer concentration begins to decrease, followed by a decrease in oligomer concentration, starting with LMWOs, which are the least stable species. The observed behavior classifies the two LMWOs as off pathway. In contrast, we consider HMWOs to be on-pathway, prefibrillar intermediates, representing structures in which nucleated conformational conversion is facilitated by high local concentrations. Aβ40 and Aβ42 M35ox take much longer to form nuclei and enter the growth phase than Aβ42 under identical reaction conditions, presumably because both the size and the concentration of HMWOs formed are much smaller.
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Affiliation(s)
- Thomas Pauly
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | | | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany.
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
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6
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Wu K, Sun W, Li D, Diao J, Xiu P. Inhibition of Amyloid Nucleation by Steric Hindrance. J Phys Chem B 2022; 126:10045-10054. [PMID: 36417323 DOI: 10.1021/acs.jpcb.2c06330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite recent experiments and simulations suggesting that small-molecule inhibitors and some post-translational modifications (e.g., glycosylation and ubiquitination) can suppress the pathogenic aggregation of proteins due to steric hindrance, the effect of steric hindrance on amyloid formation has not been systematically studied. Based on Monte Carlo simulations using a coarse-grained model for amyloidogenic proteins and a hard sphere acting as steric hindrance, we investigated how steric hindrance on proteins could affect amyloid formation, particularly two steps of primary nucleation, namely, oligomerization and conformational conversion into a β-sheet-enriched nucleus. We found that steric spheres played an inhibitory role in oligomerization with the effect proportional to the sphere radius RS, which we attributed to the decline in the nonspecific attractions between proteins. During the second step, small steric spheres facilitated the conformational conversion of proteins while large ones suppressed the conversion. The overall steric effect on amyloid nucleation was inhibitory regardless of RS. As RS increased, oligomeric assemblies changed from amorphous into sheet-like, structurally ordered species, reminiscent of the structure of amyloid fibrils. The oligomers with large RS were off-pathway with their ordered structures induced by the competition between steric hindrance and nonspecific attractions of soluble proteins. Interestingly, the equimolar mixture of proteins with and without steric hindrance amplified the sterically inhibitory effect by increasing the energy barrier of protein's conformational conversion. The physical mechanisms and biological implications of the above results are discussed. Our findings improve the current understanding of how nature regulates protein aggregation and amyloid formation by steric hindrance.
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Affiliation(s)
- Kai Wu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Wuxuepeng Sun
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Dechang Li
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Peng Xiu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
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7
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Zhang T, Pan Y, Kandapal S, Sun X, Xu B. Following the Aggregation of Human Prion Protein on Heparin Functionalized Gold Surface in Real Time. ACS APPLIED BIO MATERIALS 2022; 5:5457-5464. [PMID: 36228282 DOI: 10.1021/acsabm.2c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The aggregation of the prion protein (PrP) plays a key role in the development of prion diseases and is believed to be an autocatalytic process with a very high kinetic barrier. Intensive studies have focused on overcoming the kinetic barriers under extremely nonphysiological in vitro conditions by altering the pH of PrP solution on solid surfaces, such as gold, mica, and a lipid bilayer. Importantly, sulfated glycosaminoglycans (GAGs), including heparin, were found to be associated with PrP misfolding and aggregation, suggesting GAGs have catalytic roles in PrP aggregation processes. However, the exact role and details of GAGs in the PrP aggregation are not clear and need a thorough perusal. Here, we investigate the PrP aggregation process on a heparin functionalized gold surface by in situ, real-time monitoring of the atomic scale details of the whole aggregation process by single molecule atomic force microscopy (AFM), combining simultaneous topographic and recognition (TREC) imaging and single molecule force spectroscopy (SMFS). We observed the whole aggregation process for full-length human recombinant PrP (23-231) aggregation on the heparin modified gold surface, from the formation of oligomers, to the assembly of protofibrils and short fibers, and the formation of elongated mature fibers. Heparin is found to promote the PrP aggregation by facilitating the formation of oligomers during the early nucleation stage.
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Affiliation(s)
- Tong Zhang
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Yangang Pan
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Sneha Kandapal
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Xin Sun
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia30602, United States
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8
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Essential Components of Synthetic Infectious Prion Formation De Novo. Biomolecules 2022; 12:biom12111694. [DOI: 10.3390/biom12111694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Prion diseases are a class of neurodegenerative diseases that are uniquely infectious. Whilst their general replication mechanism is well understood, the components required for the formation and propagation of highly infectious prions are poorly characterized. The protein-only hypothesis posits that the prion protein (PrP) is the only component of the prion; however, additional co-factors are required for its assembly into infectious prions. These can be provided by brain homogenate, but synthetic lipids and non-coding RNA have also been used in vitro. Here, we review a range of experimental approaches, which generate PrP amyloid assemblies de novo. These synthetic PrP assemblies share some, but not necessarily all, properties of genuine infectious prions. We will discuss the different experimental approaches, how a prion is defined, the non-protein requirements of a prion, and provide an overview of the current state of prion amplification and generation in vitro.
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9
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Metal Ions Bound to Prion Protein Affect its Interaction with Plasminogen Activation System. Protein J 2022; 41:88-96. [PMID: 35038117 PMCID: PMC8863686 DOI: 10.1007/s10930-021-10035-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 11/22/2022]
Abstract
Prion diseases are a group of neurodegenerative diseases, which can progress rapidly. Previous data have demonstrated that prion protein (PrP) stimulates activation of plasminogen (Plg) by tissue plasminogen activator (tPA). In this study, using spectroscopic method, we aimed to determine whether PrP’s role in activating Plg is influenced by metal binding. We also investigated the region in PrP involved in binding to tPA and Plg, and whether PrP in fibrillar form behaves the same way as PrP unbound to any metal ion i.e., apo-PrP. We investigated the effect of recombinant mouse PrP (residues 23-231) refolded with nickel, manganese, copper, and a variant devoid of any metal ions, on tPA-catalyzed Plg activation. Using mutant PrP (H95A, H110A), we also investigated whether histidine residues outside the octarepeat region in PrP, which is known to bind tPA and Plg, are also involved in their binding. We demonstrated that apo-PrP is most effective at stimulating Plg. PrP refolded with nickle or manganese behave similar to apo-PrP, and PrP refolded with copper is least effective. The mutant form of PrP did not stimulate Plg activation to the same degree as apo-PrP indicating that the histidine residues outside the octarepeat region are also involved in binding to tPA and Plg. Similarly, the fibrillar form of PrP was ineffective at stimulating Plg activation. Our data suggest that upon loss of copper specifically, a structural rearrangement of PrP occurs that exposes binding sites to Plg and tPA, enhancing the stimulation of Plg activation.
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10
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Serpa JJ, Popov KI, Petrotchenko EV, Dokholyan NV, Borchers CH. Structure of prion β-oligomers as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations. Proteomics 2021; 21:e2000298. [PMID: 34482645 PMCID: PMC9285417 DOI: 10.1002/pmic.202000298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/10/2021] [Accepted: 08/27/2021] [Indexed: 11/08/2022]
Abstract
The conversion of the native monomeric cellular prion protein (PrPC ) into an aggregated pathological β-oligomeric form (PrPβ ) and an infectious form (PrPSc ) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational changes involved in the conversion are still unknown. We applied mass spectrometry combined with chemical crosslinking, hydrogen/deuterium exchange, limited proteolysis, and surface modification for the differential characterization of the native and the urea+acid-converted prion β-oligomer structures to obtain insights into the mechanisms of conversion and aggregation. For the determination of the structure of the monomer and the dimer unit of the β-oligomer, we applied a recently-developed approach for de novo protein structure determination which is based on the incorporation of zero-length and short-distance crosslinking data as intra- and inter-protein constraints in discrete molecular dynamics simulations (CL-DMD). Based on all of the structural-proteomics experimental data and the computationally predicted structures of the monomer units, we propose the potential mode of assembly of the β-oligomer. The proposed β-oligomer assembly provides a clue on the β-sheet nucleation site, and how template-based conversion of the native prion molecule occurs, growth of the prion aggregates, and maturation into fibrils may occur.
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Affiliation(s)
- Jason J Serpa
- University of Victoria -Genome British Columbia Proteomics Centre, Victoria, British Columbia, Canada
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
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11
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Chatterjee S, Salimi A, Lee JY. Unraveling the Histidine Tautomerism Effect on the Initial Stages of Prion Misfolding: New Insights from a Computational Perspective. ACS Chem Neurosci 2021; 12:3203-3213. [PMID: 34382391 DOI: 10.1021/acschemneuro.1c00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The aggregation and structural conversion of normal prion peptide (PrPC) into the pathogenic scrapie form (PrPSc), which can act as a seed to enhance prion amyloid fiber formation, is believed to be a crucial event in prionopathies. Previous research suggests that the prion monomer may play an important role in oligomer generation during disease pathogenesis. In the present study, extensive replica-exchange molecular dynamics (REMD) simulations were conducted to explore the conformational characteristics of the huPrP (125-160) monomer under the histidine tautomerism effect. Investigating the structural characteristics and fibrilization process is challenging because two histidine tautomers [Nε2-H (ε) and Nδ1-H (δ)] can occur in the open neutral state. Molecular dynamics (MD) simulation outcomes have shown that the toxic εδ and δδ isomer (containing several and broader local minima) had the highest α-helix structures, with contents of 21.11% and 21.01%, respectively, and may have a strong influence on the organizational behavior of a monomeric prion. The amino acids aspartate 20 (D20)-asparagine 29 (N29) and isoleucine 15 (I15)-histidine 16 (H16), D20-arginine 27 (R27) as well as N29 formed α-helix with the highest probabilities in the δδ and εδ isomer, accordingly. On the basis of our findings, we propose the histidine tautomerization hypothesis as a new prion accumulation mechanism, which may exist to induce the formation of prion accumulates. Overall, our tautomerism hypothesis constitutes a promising perspective for enhancing understanding of prion disease pathobiology and may help in the design of a good inhibitor.
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Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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12
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Saha D, Jana B. Kinetic and thermodynamic stability comparison for the fibrillar form of small amyloid-β(1-42) oligomers using scaled molecular dynamics. Phys Chem Chem Phys 2021; 23:16897-16908. [PMID: 34328153 DOI: 10.1039/d1cp01866c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Amyloid-β (Aβ) oligomers act as intermediates for several neurodegenerative disease-relevant fibril formations. However, gaining insight into the oligomer to fibril conversion process remains a challenge due to the transient nature of small Aβ. In this study, we probe the kinetic and thermodynamic stabilities of small Aβ(1-42) oligomers in fibrillar conformations to understand from what size these aggregates start forming stable fibrils. With no definite structures available for small Aβ42 aggregates, we have started with oligomers extracted from mature fibrils having four, five, six and nine chains stacked together, and have performed order-to-disorder transition on these systems. Using scaled molecular dynamics (sMD) simulation, the timescale for breaking the native contacts of fibrils has been compared. The results indicate that the kinetic stability of oligomers increases with size, especially at the C-terminus end beyond five-chain oligomers. The free energy of breaking the contacts at the β-sheet regions in the structures has been obtained on an unscaled potential from a free energy extrapolation (FEE) approach. The values show that although stable minima are obtained for larger oligomers due to the enhanced stability of the C-terminus ends, fully stable fibril formation may require aggregates larger than the ones considered in our study. Additionally, dissimilar kinetics for the unbinding of terminal chains across all the oligomers has been observed. The interaction energy values calculated from unscaled MD simulations reveal the crucial role of water in our observations. Our work provides the application of an easy-to-deploy method that sheds light on interactions which could be significant in the early stages of Aβ42 fibril formation.
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Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
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13
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Sangeetham SB, Engelke AD, Fodor E, Krausz SL, Tatzelt J, Welker E. The G127V variant of the prion protein interferes with dimer formation in vitro but not in cellulo. Sci Rep 2021; 11:3116. [PMID: 33542378 PMCID: PMC7862613 DOI: 10.1038/s41598-021-82647-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/10/2020] [Indexed: 01/30/2023] Open
Abstract
Scrapie prion, PrPSc, formation is the central event of all types of transmissible spongiform encephalopathies (TSEs), while the pathway with possible intermediates and their mechanism of formation from the normal isoform of prion (PrP), remains not fully understood. Recently, the G127V variant of the human PrP is reported to render the protein refractory to transmission of TSEs, via a yet unknown mechanism. Molecular dynamics studies suggested that this mutation interferes with the formation of PrP dimers. Here we analyze the dimerization of 127G and 127VPrP, in both in vitro and a mammalian cell culture system. Our results show that while molecular dynamics may capture the features affecting dimerization in vitro, G127V inhibiting dimer formation of PrP, these are not evidenced in a more complex cellular system.
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Affiliation(s)
- Sudheer Babu Sangeetham
- Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Dugonics square 13, Szeged, 6720, Hungary
| | - Anna Dorothee Engelke
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
- School of Ph.D. Studies, Semmelweis University, Budapest, 1085, Hungary
- Aktogen Hungary Ltd., Kecskemét, 6000, Hungary
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany.
- Cluster of Excellence RESOLV, Bochum, Germany.
| | - Ervin Welker
- Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary.
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14
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Orvay F, Cerdá J, Rotger C, Ortí E, Aragó J, Costa A, Soberats B. Influence of the Z/E Isomerism on the Pathway Complexity of a Squaramide-Based Macrocycle. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006133. [PMID: 33448095 DOI: 10.1002/smll.202006133] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/25/2020] [Indexed: 05/25/2023]
Abstract
The rising interest on pathway complexity in supramolecular polymerization has prompted the finding of novel monomer designs able to stabilize kinetically trapped species and generate supramolecular polymorphs. In the present work, the exploitation of the Z/E (geometrical) isomerism of squaramide (SQ) units to produce various self-assembled isoforms and complex supramolecular polymerization pathways in methylcyclohexane/CHCl3 mixtures is reported for the first time. This is achieved by using a new bissquaramidic macrocycle (MSq) that self-assembles into two markedly different thermodynamic aggregates, AggA (discrete cyclic structures) and AggB (fibrillar structures), depending on the solvent composition and concentration. Remarkably, UV-vis, 1 H NMR, and FT-IR experiments together with quantum-chemical calculations indicate that these two distinct aggregates are formed via two different hydrogen bonding patterns (side-to-side in AggA and head-to-tail in AggB) due to different conformations in the SQ units (Z,E in AggA and Z,Z in AggB). The ability of MSq to supramolecularly polymerize into two distinct aggregates is utilized to induce the kinetic-to-thermodynamic transformation from AggA to AggB, which occurs via an on-pathway mechanism. It is believed that this system provides new insights for the design of potential supramolecular polymorphic materials by using squaramide units.
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Affiliation(s)
- Francisca Orvay
- Department of Chemistry, University of the Balearic Islands, Cra. Valldemossa, Km. 7.5, Palma de Mallorca, 07122, Spain
| | - Jesús Cerdá
- Instituto de Ciencia Molecular, Universidad de Valencia, Paterna, 46980, Spain
| | - Carmen Rotger
- Department of Chemistry, University of the Balearic Islands, Cra. Valldemossa, Km. 7.5, Palma de Mallorca, 07122, Spain
| | - Enrique Ortí
- Instituto de Ciencia Molecular, Universidad de Valencia, Paterna, 46980, Spain
| | - Juan Aragó
- Instituto de Ciencia Molecular, Universidad de Valencia, Paterna, 46980, Spain
| | - Antonio Costa
- Department of Chemistry, University of the Balearic Islands, Cra. Valldemossa, Km. 7.5, Palma de Mallorca, 07122, Spain
| | - Bartolome Soberats
- Department of Chemistry, University of the Balearic Islands, Cra. Valldemossa, Km. 7.5, Palma de Mallorca, 07122, Spain
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15
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From Posttranslational Modifications to Disease Phenotype: A Substrate Selection Hypothesis in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22020901. [PMID: 33477465 PMCID: PMC7830165 DOI: 10.3390/ijms22020901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 11/16/2022] Open
Abstract
A number of neurodegenerative diseases including prion diseases, tauopathies and synucleinopathies exhibit multiple clinical phenotypes. A diversity of clinical phenotypes has been attributed to the ability of amyloidogenic proteins associated with a particular disease to acquire multiple, conformationally distinct, self-replicating states referred to as strains. Structural diversity of strains formed by tau, α-synuclein or prion proteins has been well documented. However, the question how different strains formed by the same protein elicit different clinical phenotypes remains poorly understood. The current article reviews emerging evidence suggesting that posttranslational modifications are important players in defining strain-specific structures and disease phenotypes. This article put forward a new hypothesis referred to as substrate selection hypothesis, according to which individual strains selectively recruit protein isoforms with a subset of posttranslational modifications that fit into strain-specific structures. Moreover, it is proposed that as a result of selective recruitment, strain-specific patterns of posttranslational modifications are formed, giving rise to unique disease phenotypes. Future studies should define whether cell-, region- and age-specific differences in metabolism of posttranslational modifications play a causative role in dictating strain identity and structural diversity of strains of sporadic origin.
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16
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Ashrafian H, Zadeh EH, Khan RH. Review on Alzheimer's disease: Inhibition of amyloid beta and tau tangle formation. Int J Biol Macromol 2020; 167:382-394. [PMID: 33278431 DOI: 10.1016/j.ijbiomac.2020.11.192] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/18/2020] [Accepted: 11/28/2020] [Indexed: 12/19/2022]
Abstract
It is reported that approximately 40 million people are suffering from dementia, globally. Dementia is a group of symptoms that affect neurons and cause some mental disorders, such as losing memory. Alzheimer's disease (AD) which is known as the most common cause of dementia, is one of the top medical care concerns across the world. Although the exact sources of the disease are not understood, is it believed that aggregation of amyloid-beta (Aβ) outside of neuron cells and tau aggregation or neurofibrillary tangles (NFTs) formation inside the cell may play crucial roles. In this paper, we are going to review studies that targeted inhibition of amyloid plaque and tau protein tangle formation, to suppress or postpone AD.
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Affiliation(s)
- Hossein Ashrafian
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA; Department of Chemistry, Sharif University of Technology, Tehran, Iran.
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17
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Nie J, Chen Z. Protein-Based Nano-Vessels Facilitates the Victoria Blue B Mediated Inhibition of Amyloid Fibrillation. Macromol Rapid Commun 2020; 41:e2000368. [PMID: 33015910 DOI: 10.1002/marc.202000368] [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: 07/09/2020] [Revised: 09/04/2020] [Indexed: 11/08/2022]
Abstract
Amyloid fibrils are associated with a number of serious and incurable diseases. The understanding of the pathogenic formation of amyloid proteins is progressing. Nonetheless, no treatment is available to deal with amyloid diseases. It is reported here that victoria blue B (VBB) contains an intrinsic marginal inhibitory activity toward protein fibrillation. Moreover, when VBB is co-assembled with scaffold proteins to form fluorescent protein nano-vessels (VBB-FPNs), these complexes show much improved fibrillation inhibitory effects. VBB-FPNs can effectively inhibit lysozyme fibrils formation likely through delaying the nucleation and elongation in a concentration-dependent manner as shown by fluorescent assay, circular dichroism, transmission electron microscopy, and atomic force microscopy. This work describes a new inhibitor of protein fibrillation and provides a new means to enhance the inhibition efficiency of given inhibitors, thus affording a fresh angle to modulate protein fibrillation.
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Affiliation(s)
- Junlian Nie
- J. Nie, Prof. Z. Chen, Institute of Theoretical Chemistry and College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Zhijun Chen
- J. Nie, Prof. Z. Chen, Institute of Theoretical Chemistry and College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
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18
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Admane N, Srivastava A, Jamal S, Kundu B, Grover A. Protective Effects of a Neurohypophyseal Hormone Analogue on Prion Aggregation, Cellular Internalization, and Toxicity. ACS Chem Neurosci 2020; 11:2422-2430. [PMID: 31407881 DOI: 10.1021/acschemneuro.9b00299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Herein, we report novel neuroprotective activity of the neurohypophyseal hormone analogue desmopressin (DDAVP) against toxic conformations of human prion protein. Systematic analysis using biophysical techniques in conjunction with surface plasmon resonance, high-end microscopy, conformational antibodies, and cell-based assays demonstrated DDAVP's specific binding and potent antiaggregating effects on prion protein (rPrPres). In addition to subjugating conformational conversion of rPrPres into oligomeric forms, DDAVP also exhibits potent fibril modulatory effects. It eventually ameliorated neuronal toxicity of rPrPres oligomers by significantly reducing their cellular internalization. Molecular dynamics simulations showed that DDAVP prevents β-sheet transitions in the N-terminal amyloidogenic region of prion and induces antagonistic mobilities in its α2-α3 and β2-α2 loop regions. Collectively, our data proposes DDAVP as a new structural motif for rational drug discovery against prion diseases.
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Affiliation(s)
- Nikita Admane
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Ankit Srivastava
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Salma Jamal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
| | - Bishwajit Kundu
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India − 110016
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India − 110067
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19
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Huin C, Cronier S, Guégan P, Béringue V, Rezaei H, Noinville S. Conformation-dependent membrane permeabilization by neurotoxic PrP oligomers: The role of the H2H3 oligomerization domain. Arch Biochem Biophys 2020; 692:108517. [PMID: 32738196 DOI: 10.1016/j.abb.2020.108517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/08/2020] [Accepted: 07/26/2020] [Indexed: 12/11/2022]
Abstract
The relationship between prion propagation and the generation of neurotoxic species and clinical onset remains unclear. Several converging lines of evidence suggest that interactions with lipids promote various precursors to form aggregation-prone states that are involved in amyloid fibrils. Here, we compared the cytotoxicities of different soluble isolated oligomeric constructs from murine full-length PrP and from the restricted helical H2H3 domain with their effects on lipid vesicles. The helical H2H3 domain is suggested to be the minimal region of PrP involved in the oligomerization process. The discrete PrP oligomers of both the full-length sequence and the H2H3 domain have de novo β-sheeted structure when interacting with the membrane. They were shown to permeabilize synthetic negatively charged vesicles in a dose-dependent manner. Restricting the polymerization domain of the full-length PrP to the H2H3 helices strongly diminished the ability of the corresponding oligomers to associate with the lipid vesicles. Furthermore, the membrane impairment mechanism occurs differently for the full-length PrP oligomers and the H2H3 helices, as shown by dye-release and black lipid membrane experiments. The membrane damage caused by the full-length PrP oligomers is correlated to their neuronal toxicity at submicromolar concentrations, as shown by cell culture assays. Although oligomers of synthetic H2H3 could compromise in vitro cell homeostasis, they followed a membrane-disruptive pattern that was different from the full-length oligomers, as revealed by the role of PrPC in cell viability assays.
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Affiliation(s)
- Cécile Huin
- Sorbonne Universités, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, F-75005, Paris, France; University of Evry, F-91025, Evry, France
| | - Sabrina Cronier
- UR892, Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
| | - Philippe Guégan
- Sorbonne Universités, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, F-75005, Paris, France
| | - Vincent Béringue
- UR892, Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
| | - Human Rezaei
- UR892, Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France
| | - Sylvie Noinville
- UR892, Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique (INRA), Jouy-en-Josas, France; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR8233, MONARIS, Université Pierre et Marie Curie, Paris, France.
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20
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Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chem Sci 2020; 11:6236-6247. [PMID: 32953019 PMCID: PMC7480182 DOI: 10.1039/c9sc06501f] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation.
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Affiliation(s)
- Alexander J Dear
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Anđela Šarić
- Department of Physics and Astronomy , Institute for the Physics of Living Systems , University College London , Gower Street , London WC1E 6BT , UK
- MRC Laboratory for Molecular Cell Biology , University College London , Gower St, WC1E 6BT , London , UK
| | - Thomas C T Michaels
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , MA 02138 , USA
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics , Aarhus University , Høegh-Guldbergs Gade 6B , DK-8000 Aarhus C , Denmark
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
- Cavendish Laboratory , Department of Physics , University of Cambridge , J J Thomson Avenue , Cambridge CB3 0HE , UK .
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21
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Mishra A, Korlepara DB, Balasubramanian S, George SJ. Bioinspired, ATP-driven co-operative supramolecular polymerization and its pathway dependence. Chem Commun (Camb) 2020; 56:1505-1508. [PMID: 31917382 DOI: 10.1039/c9cc08790g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A bio-inspired, ATP-driven nucleation growth assembly is demonstrated using an amphiphilic naphthalene diimide (NDI) derivative appended with guanidinium receptors to promote specific salt-bridge type interaction with nucleotide phosphates. Detailed spectroscopic and microscopic probing revealed a pathway-dependent co-operative self-assembly to yield two-dimensional and scrolled nano-tubular bilayer assemblies under kinetic and thermodynamic conditions, respectively.
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Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory, New Chemistry Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India.
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22
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Helmers I, Niehues M, Kartha KK, Ravoo BJ, Fernández G. Synergistic repulsive interactions trigger pathway complexity. Chem Commun (Camb) 2020; 56:8944-8947. [DOI: 10.1039/d0cc03603j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We demonstrate the impact of synergistic repulsive interactions on pathway complexity in aqueous media.
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Affiliation(s)
- Ingo Helmers
- Organisch-Chemisches Institut
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Maximilian Niehues
- Organisch-Chemisches Institut
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Kalathil K. Kartha
- Organisch-Chemisches Institut
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Bart Jan Ravoo
- Organisch-Chemisches Institut
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Gustavo Fernández
- Organisch-Chemisches Institut
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
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23
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Karamanos TK, Jackson MP, Calabrese AN, Goodchild SC, Cawood EE, Thompson GS, Kalverda AP, Hewitt EW, Radford SE. Structural mapping of oligomeric intermediates in an amyloid assembly pathway. eLife 2019; 8:46574. [PMID: 31552823 PMCID: PMC6783270 DOI: 10.7554/elife.46574] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/24/2019] [Indexed: 01/02/2023] Open
Abstract
Transient oligomers are commonly formed in the early stages of amyloid assembly. Determining the structure(s) of these species and defining their role(s) in assembly is key to devising new routes to control disease. Here, using a combination of chemical kinetics, NMR spectroscopy and other biophysical methods, we identify and structurally characterize the oligomers required for amyloid assembly of the protein ΔN6, a truncation variant of human β2-microglobulin (β2m) found in amyloid deposits in the joints of patients with dialysis-related amyloidosis. The results reveal an assembly pathway which is initiated by the formation of head-to-head non-toxic dimers and hexamers en route to amyloid fibrils. Comparison with inhibitory dimers shows that precise subunit organization determines amyloid assembly, while dynamics in the C-terminal strand hint to the initiation of cross-β structure formation. The results provide a detailed structural view of early amyloid assembly involving structured species that are not cytotoxic.
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Affiliation(s)
- Theodoros K Karamanos
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Matthew P Jackson
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Antonio N Calabrese
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sophia C Goodchild
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Emma E Cawood
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Gary S Thompson
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Arnout P Kalverda
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Eric W Hewitt
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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24
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Aliprandi A, Capaldo L, Bobica C, Silvestrini S, De Cola L. Effects of the Molecular Design on the Supramolecular Organization of Luminescent Pt(II) Complexes. Isr J Chem 2019. [DOI: 10.1002/ijch.201900047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alessandro Aliprandi
- Laboratoire de Chimie et des Biomatériaux Supramoléculaires Institut de Science et d'Ingénierie Supramoléculaires (UMR 7006)Université de Strasbourg & CNRS 8 allée Gaspard Monge 67000 Strasbourg France
| | - Luca Capaldo
- Laboratoire de Chimie et des Biomatériaux Supramoléculaires Institut de Science et d'Ingénierie Supramoléculaires (UMR 7006)Université de Strasbourg & CNRS 8 allée Gaspard Monge 67000 Strasbourg France
| | - Carla Bobica
- Laboratoire de Chimie et des Biomatériaux Supramoléculaires Institut de Science et d'Ingénierie Supramoléculaires (UMR 7006)Université de Strasbourg & CNRS 8 allée Gaspard Monge 67000 Strasbourg France
| | - Simone Silvestrini
- Laboratoire de Chimie et des Biomatériaux Supramoléculaires Institut de Science et d'Ingénierie Supramoléculaires (UMR 7006)Université de Strasbourg & CNRS 8 allée Gaspard Monge 67000 Strasbourg France
| | - Luisa De Cola
- Laboratoire de Chimie et des Biomatériaux Supramoléculaires Institut de Science et d'Ingénierie Supramoléculaires (UMR 7006)Université de Strasbourg & CNRS 8 allée Gaspard Monge 67000 Strasbourg France
- Institut für Nanotechnologie (INT)Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldschaffen Germany
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25
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Zhou S, Shi D, Liu X, Yao X, Da LT, Liu H. pH-Induced Misfolding Mechanism of Prion Protein: Insights from Microsecond-Accelerated Molecular Dynamics Simulations. ACS Chem Neurosci 2019; 10:2718-2729. [PMID: 31070897 DOI: 10.1021/acschemneuro.8b00582] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The conformational transition of prion protein (PrP) from a native form PrPC to a pathological isoform PrPSc is the main cause of a number of prion diseases in human and animals. Thus, understanding the molecular basis of conformational transition of PrP will be valuable for unveiling the etiology of PrP-related diseases. Here, to explore the potential misfolding mechanism of PrP under the acidic condition, which is known to promote PrP misfolding and trigger its aggregation, the conventional and accelerated molecular dynamics (MD) simulations combined with the Markov state model (MSM) analysis were performed. The conventional MD simulations reveal that, at an acidic pH, the globular domain of PrP is partially unfolded, particularly for the α2 C-terminus. Structural analysis of the key macrostates obtained by MSM indicates that the α2 C-terminus and the β2-α2 loop may serve as important sites for the pH-induced PrP misfolding. Meanwhile, the α1 may also participate in the pH-induced structural conversion by moving away from the α2-α3 subdomain. Notably, dynamical network analysis of the key metastable states indicates that the protonated H187 weakens the interactions between the α2 C-terminus, α1-β2 loop, and α2-α3 loop, leading these domains, especially the α2 C-terminus, to become unstable and to begin to misfold. Therefore, the α2 C-terminus plays a key role in the PrP misfolding process and serves as a potential site for drug targeting. Overall, our findings can deepen the understanding of the pathogenesis related to PrP and provide useful guidance for the future drug discovery.
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Affiliation(s)
- Shuangyan Zhou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Chongqing Key Laboratory on Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai 200240, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
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26
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Sang JC, Lee JE, Dear AJ, De S, Meisl G, Thackray AM, Bujdoso R, Knowles TPJ, Klenerman D. Direct observation of prion protein oligomer formation reveals an aggregation mechanism with multiple conformationally distinct species. Chem Sci 2019; 10:4588-4597. [PMID: 31123569 PMCID: PMC6492631 DOI: 10.1039/c8sc05627g] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
Abstract
The aggregation of the prion protein (PrP) plays a key role in the development of prion diseases. In the past decade, a similar process has been associated with other proteins, such as Aβ, tau, and α-synuclein, which participate in other neurodegenerative diseases. It is increasingly recognized that the small oligomeric species of aggregates can play an important role in the development of prion diseases. However, determining the nature of the oligomers formed during the aggregation process has been experimentally difficult due to the lack of suitable methods capable of the detection and characterization of the low level of oligomers that may form. To address this problem, we have utilized single-aggregate methods to study the early events associated with aggregation of recombinant murine PrP in vitro to approach the bona fide process in vivo. PrP aggregation resulted in the formation of thioflavin T (ThT)-inactive and ThT-active species of oligomers. The ThT-active oligomers undergo conversion from a Proteinase K (PK)-sensitive to PK-resistant conformer, from which mature fibrils can eventually emerge. Overall, our results show that single-aggregate methods can provide structural and mechanistic insights into PrP aggregation, identify the potential species that mediates cytotoxicity, and reveal that a range of distinct oligomeric species with different properties is formed during prion protein aggregation.
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Affiliation(s)
- Jason C Sang
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Ji-Eun Lee
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Alexander J Dear
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Suman De
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - Alana M Thackray
- Department of Veterinary Medicine , University of Cambridge , Madingley Road , Cambridge , CB3 0ES , UK
| | - Raymond Bujdoso
- Department of Veterinary Medicine , University of Cambridge , Madingley Road , Cambridge , CB3 0ES , UK
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
| | - David Klenerman
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK .
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27
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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28
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Scialò C, De Cecco E, Manganotti P, Legname G. Prion and Prion-Like Protein Strains: Deciphering the Molecular Basis of Heterogeneity in Neurodegeneration. Viruses 2019; 11:E261. [PMID: 30875755 PMCID: PMC6466326 DOI: 10.3390/v11030261] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022] Open
Abstract
Increasing evidence suggests that neurodegenerative disorders share a common pathogenic feature: the presence of deposits of misfolded proteins with altered physicochemical properties in the Central Nervous System. Despite a lack of infectivity, experimental data show that the replication and propagation of neurodegenerative disease-related proteins including amyloid-β (Aβ), tau, α-synuclein and the transactive response DNA-binding protein of 43 kDa (TDP-43) share a similar pathological mechanism with prions. These observations have led to the terminology of "prion-like" to distinguish between conditions with noninfectious characteristics but similarities with the prion replication and propagation process. Prions are considered to adapt their conformation to changes in the context of the environment of replication. This process is known as either prion selection or adaptation, where a distinct conformer present in the initial prion population with higher propensity to propagate in the new environment is able to prevail over the others during the replication process. In the last years, many studies have shown that prion-like proteins share not only the prion replication paradigm but also the specific ability to aggregate in different conformations, i.e., strains, with relevant clinical, diagnostic and therapeutic implications. This review focuses on the molecular basis of the strain phenomenon in prion and prion-like proteins.
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Affiliation(s)
- Carlo Scialò
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy.
| | - Elena De Cecco
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy.
| | - Paolo Manganotti
- Clinical Unit of Neurology, Department of Medicine, Surgery and Health Sciences, University Hospital and Health Services of Trieste, University of Trieste, 34149 Trieste, Italy.
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy.
- ELETTRA Sincrotrone Trieste S.C.p.A, Basovizza, 34149 Trieste, Italy.
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29
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Burke CM, Walsh DJ, Steele AD, Agrimi U, Di Bari MA, Watts JC, Supattapone S. Full restoration of specific infectivity and strain properties from pure mammalian prion protein. PLoS Pathog 2019; 15:e1007662. [PMID: 30908557 PMCID: PMC6448948 DOI: 10.1371/journal.ppat.1007662] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/04/2019] [Accepted: 02/27/2019] [Indexed: 12/26/2022] Open
Abstract
The protein-only hypothesis predicts that infectious mammalian prions are composed solely of PrPSc, a misfolded conformer of the normal prion protein, PrPC. However, protein-only PrPSc preparations lack significant levels of prion infectivity, leading to the alternative hypothesis that cofactor molecules are required to form infectious prions. Here, we show that prions with parental strain properties and full specific infectivity can be restored from protein-only PrPSc in vitro. The restoration reaction is rapid, potent, and requires bank vole PrPC substrate, post-translational modifications, and cofactor molecules. To our knowledge, this represents the first report in which the essential properties of an infectious mammalian prion have been restored from pure PrP without adaptation. These findings provide evidence for a unified hypothesis of prion infectivity in which the global structure of protein-only PrPSc accurately stores latent infectious and strain information, but cofactor molecules control a reversible switch that unmasks biological infectivity.
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Affiliation(s)
- Cassandra M. Burke
- Departments of Biochemistry and Cell Biology at Darthmouth, Hanover, New Hampshire, United States of America
| | - Daniel J. Walsh
- Departments of Biochemistry and Cell Biology at Darthmouth, Hanover, New Hampshire, United States of America
| | - Alexander D. Steele
- Departments of Biochemistry and Cell Biology at Darthmouth, Hanover, New Hampshire, United States of America
| | - Umberto Agrimi
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Michele Angelo Di Bari
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Joel C. Watts
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Surachai Supattapone
- Departments of Biochemistry and Cell Biology at Darthmouth, Hanover, New Hampshire, United States of America
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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30
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Rösener NS, Gremer L, Reinartz E, König A, Brener O, Heise H, Hoyer W, Neudecker P, Willbold D. A d-enantiomeric peptide interferes with heteroassociation of amyloid-β oligomers and prion protein. J Biol Chem 2018; 293:15748-15764. [PMID: 30131337 PMCID: PMC6187637 DOI: 10.1074/jbc.ra118.003116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects millions of people worldwide. One AD hallmark is the aggregation of β-amyloid (Aβ) into soluble oligomers and insoluble fibrils. Several studies have reported that oligomers rather than fibrils are the most toxic species in AD progression. Aβ oligomers bind with high affinity to membrane-associated prion protein (PrP), leading to toxic signaling across the cell membrane, which makes the Aβ-PrP interaction an attractive therapeutic target. Here, probing this interaction in more detail, we found that both full-length, soluble human (hu) PrP(23-230) and huPrP(23-144), lacking the globular C-terminal domain, bind to Aβ oligomers to form large complexes above the megadalton size range. Following purification by sucrose density-gradient ultracentrifugation, the Aβ and huPrP contents in these heteroassemblies were quantified by reversed-phase HPLC. The Aβ:PrP molar ratio in these assemblies exhibited some limited variation depending on the molar ratio of the initial mixture. Specifically, a molar ratio of about four Aβ to one huPrP in the presence of an excess of huPrP(23-230) or huPrP(23-144) suggested that four Aβ units are required to form one huPrP-binding site. Of note, an Aβ-binding all-d-enantiomeric peptide, RD2D3, competed with huPrP for Aβ oligomers and interfered with Aβ-PrP heteroassembly in a concentration-dependent manner. Our results highlight the importance of multivalent epitopes on Aβ oligomers for Aβ-PrP interactions and have yielded an all-d-peptide-based, therapeutically promising agent that competes with PrP for these interactions.
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Affiliation(s)
- Nadine S Rösener
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lothar Gremer
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Elke Reinartz
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
| | - Anna König
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Oleksandr Brener
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Henrike Heise
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Philipp Neudecker
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Willbold
- From the Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
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31
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Ladner-Keay CL, Ross L, Perez-Pineiro R, Zhang L, Bjorndahl TC, Cashman N, Wishart DS. A simple in vitro assay for assessing the efficacy, mechanisms and kinetics of anti-prion fibril compounds. Prion 2018; 12:280-300. [PMID: 30223704 PMCID: PMC6277192 DOI: 10.1080/19336896.2018.1525254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/01/2018] [Accepted: 09/11/2018] [Indexed: 10/28/2022] Open
Abstract
Prion diseases are caused by the conversion of normal cellular prion proteins (PrP) into lethal prion aggregates. These prion aggregates are composed of proteinase K (PK) resistant fibrils and comparatively PK-sensitive oligomers. Currently there are no anti-prion pharmaceuticals available to treat or prevent prion disease. Methods of discovering anti-prion molecules rely primarily on relatively complex cell-based, tissue slice or animal-model assays that measure the effects of small molecules on the formation of PK-resistant prion fibrils. These assays are difficult to perform and do not detect the compounds that directly inhibit oligomer formation or alter prion conversion kinetics. We have developed a simple cell-free method to characterize the impact of anti-prion fibril compounds on both the oligomer and fibril formation. In particular, this assay uses shaking-induced conversion (ShIC) of recombinant PrP in a 96-well format and resolution enhanced native acidic gel electrophoresis (RENAGE) to generate, assess and detect PrP fibrils in a high throughput fashion. The end-point PrP fibrils from this assay can be further characterized by PK analysis and negative stain transmission electron microscopy (TEM). This cell-free, gel-based assay generates metrics to assess anti-prion fibril efficacy and kinetics. To demonstrate its utility, we characterized the action of seven well-known anti-prion molecules: Congo red, curcumin, GN8, quinacrine, chloropromazine, tetracycline, and TUDCA (taurourspdeoxycholic acid), as well as four suspected anti-prion compounds: trans-resveratrol, rosmarinic acid, myricetin and ferulic acid. These findings suggest that this in vitro assay could be useful in identifying and comprehensively assessing novel anti-prion fibril compounds. Abbreviations: PrP, prion protein; PK, proteinase K; ShIC, shaking-induced conversion; RENAGE, resolution enhanced native acidic gel electrophoresis; TEM, transmission electron microscopy; TUDCA, taurourspdeoxycholic acid; BSE, bovine spongiform encephalopathy; CWD, chronic wasting disease; CJD, Creutzfeldt Jakob disease; GSS, Gerstmann-Sträussler-Scheinker syndrome; FFI, fatal familial insomnia; PrPc, cellular prion protein; recPrPC, recombinant monomeric prion protein; PrPSc, infectious particle of misfolded prion protein; RT-QuIC, real-time quaking-induced conversion; PMCA, Protein Misfolding Cyclic Amplification; LPS, lipopolysaccharide; EGCG, epigallocatechin gallate; GN8, 2-pyrrolidin-1-yl-N-[4-[4-(2-pyrrolidin-1-yl-acetylamino)-benzyl]-phenyl]-acetamide; DMSO, dimethyl sulfoxide; ScN2A, scrapie infected neuroblastoma cells; IC50, inhibitory concentration for 50% reduction; recMoPrP 23-231, recombinant full-length mouse prion protein residues 23-231; EDTA; PICUP, photo-induced cross-linking of unmodified protein; BSA, bovine serum albumin;; PMSF, phenylmethanesulfonyl fluoride.
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Affiliation(s)
| | - Li Ross
- Brain Research Centre, University of British Columbia, Vancouver, Canada
| | | | - Lun Zhang
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Trent C. Bjorndahl
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Neil Cashman
- Brain Research Centre, University of British Columbia, Vancouver, Canada
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- Department of Computing Science, University of Alberta, Edmonton, Canada
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32
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Makarava N, Savtchenko R, Lasch P, Beekes M, Baskakov IV. Preserving prion strain identity upon replication of prions in vitro using recombinant prion protein. Acta Neuropathol Commun 2018; 6:92. [PMID: 30208966 PMCID: PMC6134792 DOI: 10.1186/s40478-018-0597-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 11/24/2022] Open
Abstract
Last decade witnessed an enormous progress in generating authentic infectious prions or PrPSc in vitro using recombinant prion protein (rPrP). Previous work established that rPrP that lacks posttranslational modification is able to support replication of highly infectious PrPSc with assistance of cofactors of polyanionic nature and/or lipids. Unexpectedly, previous studies also revealed that seeding of rPrP by brain-derived PrPSc gave rise to new prion strains with new disease phenotypes documenting loss of a strain identity upon replication in rPrP substrate. Up to now, it remains unclear whether prion strain identity can be preserved upon replication in rPrP. The current study reports that faithful replication of hamster strain SSLOW could be achieved in vitro using rPrP as a substrate. We found that a mixture of phosphatidylethanolamine (PE) and synthetic nucleic acid polyA was sufficient for stable replication of hamster brain-derived SSLOW PrPSc in serial Protein Misfolding Cyclic Amplification (sPMCA) that uses hamster rPrP as a substrate. The disease phenotype generated in hamsters upon transmission of recombinant PrPSc produced in vitro was strikingly similar to the original SSLOW diseases phenotype with respect to the incubation time to disease, as well as clinical, neuropathological and biochemical features. Infrared microspectroscopy (IR-MSP) indicated that PrPSc produced in animals upon transmission of recombinant PrPSc is structurally similar if not identical to the original SSLOW PrPSc. The current study is the first to demonstrate that rPrP can support replication of brain-derived PrPSc while preserving its strain identity. In addition, the current work is the first to document that successful propagation of a hamster strain could be achieved in vitro using hamster rPrP.
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33
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Sengupta I, Udgaonkar JB. Structural mechanisms of oligomer and amyloid fibril formation by the prion protein. Chem Commun (Camb) 2018; 54:6230-6242. [PMID: 29789820 DOI: 10.1039/c8cc03053g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Misfolding and aggregation of the prion protein is responsible for multiple neurodegenerative diseases. Works from several laboratories on folding of both the WT and multiple pathogenic mutant variants of the prion protein have identified several structurally dissimilar intermediates, which might be potential precursors to misfolding and aggregation. The misfolded aggregates themselves are morphologically distinct, critically dependent on the solution conditions under which they are prepared, but always β-sheet rich. Despite the lack of an atomic resolution structure of the infectious pathogenic agent in prion diseases, several low resolution models have identified the β-sheet rich core of the aggregates formed in vitro, to lie in the α2-α3 subdomain of the prion protein, albeit with local stabilities that vary with the type of aggregate. This feature article describes recent advances in the investigation of in vitro prion protein aggregation using multiple spectroscopic probes, with particular focus on (1) identifying aggregation-prone conformations of the monomeric protein, (2) conditions which trigger misfolding and oligomerization, (3) the mechanism of misfolding and aggregation, and (4) the structure of the misfolded intermediates and final aggregates.
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Affiliation(s)
- Ishita Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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34
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Zheng T, Feng H, van den Broek JM, Rahimi K, Kuehne AJC, de Vries R, Sprakel J. Controlling the Hierarchical Assembly of π-Conjugated Oligoelectrolytes. Macromol Rapid Commun 2018; 39:e1800284. [PMID: 30027644 DOI: 10.1002/marc.201800284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/14/2018] [Indexed: 01/29/2023]
Abstract
Here, a means of controlling the assembly pathways of p-conjugated oligoelectrolytes into supramolecular fibers and microtubes is presented, and it is shown how the addition of small end-caps to well-defined and pH-responsive conjugated oligomers can alter the balance between repulsive and attractive supramolecular forces and enables control of the morphology of the hierarchical assembly process. The assembly stages from nuclei to protofibers are evidenced and a hypothesis on the mechanism of microtubes formation using a combination of analytical methods is provided, revealing different degrees of order at different scales along the structural hierarchy.
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Affiliation(s)
- Tingting Zheng
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Huanhuan Feng
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Johanna M van den Broek
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Khosrow Rahimi
- DWI - Leibniz Institute for Interactive Materials, RWTH Aachen University, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Alexander J C Kuehne
- DWI - Leibniz Institute for Interactive Materials, RWTH Aachen University, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Renko de Vries
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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35
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Sangeetham SB, Huszár K, Bencsura P, Nyeste A, Hunyadi-Gulyás É, Fodor E, Welker E. Interrogating the Dimerization Interface of the Prion Protein Via Site-Specific Mutations to p-Benzoyl-L-Phenylalanine. J Mol Biol 2018; 430:2784-2801. [PMID: 29778603 DOI: 10.1016/j.jmb.2018.05.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 01/10/2023]
Abstract
Transmissible spongiform encephalopathies are centered on the conformational transition of the prion protein from a mainly helical, monomeric structure to a β-sheet rich ordered aggregate. Experiments indicate that the main infectious and toxic species in this process are however shorter oligomers, formation of which from the monomers is yet enigmatic. Here, we created 25 variants of the mouse prion protein site-specifically containing one genetically-incorporated para-benzoyl-phenylalanine (pBpa), a cross-linkable non-natural amino acid, in order to interrogate the interface of a prion protein-dimer, which might lie on the pathway of oligomerization. Our results reveal that the N-terminal part of the prion protein, especially regions around position 127 and 107, is integral part of the dimer interface. These together with additional pBpa-containing variants of mPrP might also facilitate to gain more structural insights into oligomeric and fibrillar prion protein species including the pathological variants.
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Affiliation(s)
- Sudheer Babu Sangeetham
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Krisztina Huszár
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Petra Bencsura
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Antal Nyeste
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary; ProteoScientia Ltd., Cserhátszentiván, Hungary
| | - Éva Hunyadi-Gulyás
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ervin Welker
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary; Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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36
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Singh A, Joseph JP, Gupta D, Sarkar I, Pal A. Pathway driven self-assembly and living supramolecular polymerization in an amyloid-inspired peptide amphiphile. Chem Commun (Camb) 2018; 54:10730-10733. [DOI: 10.1039/c8cc06266h] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Temperature dependent stepwise self-assembly and seeded supramolecular polymerization of a peptide amphiphile form metastable nanoparticles to single nanofibers or twisted bundles, to render a mechanically tunable hydrogel.
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Affiliation(s)
| | | | | | | | - Asish Pal
- Institute of Nano Science and Technology
- Mohali
- India
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Sandberg A, Nyström S. Purification and Fibrillation of Recombinant Human Amyloid-β, Prion Protein, and Tau Under Native Conditions. Methods Mol Biol 2018; 1779:147-166. [PMID: 29886532 DOI: 10.1007/978-1-4939-7816-8_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein misfolding, aggregation, and amyloid formation is involved in a large number of diseases. Recombinantly expressed proteins to study the amyloid fibril formation process are important for mechanistic studies. We here report protocols for production, purification, and fibrillation of three different proteins commonly found in cerebral amyloid; Aβ and Tau found in Alzheimer's disease, Chronic traumatic brain injury, Corticobasal degeneration, and Progressive Supranuclear Palsy and human prion protein found in Creutzfeldt-Jakob's disease. The three protocols have in common that the protein is in a pH-neutral phosphate saline buffer during fibrillation to mimic their endogenous near physiological environment.
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Affiliation(s)
- Alexander Sandberg
- Chemistry, IFM-Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Sofie Nyström
- Chemistry, IFM-Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.
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38
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In Vitro Approach To Identify Key Amino Acids in Low Susceptibility of Rabbit Prion Protein to Misfolding. J Virol 2017; 91:JVI.01543-17. [PMID: 28978705 DOI: 10.1128/jvi.01543-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/22/2017] [Indexed: 01/10/2023] Open
Abstract
Prion diseases, or transmissible spongiform encephalopathies (TSEs), are a group of rare progressive neurodegenerative disorders caused by an abnormally folded prion protein (PrPSc). This is capable of transforming the normal cellular prion protein (PrPC) into new infectious PrPSc Interspecies prion transmissibility studies performed by experimental challenge and the outbreak of bovine spongiform encephalopathy that occurred in the late 1980s and 1990s showed that while some species (sheep, mice, and cats) are readily susceptible to TSEs, others are apparently resistant (rabbits, dogs, and horses) to the same agent. To study the mechanisms of low susceptibility to TSEs of certain species, the mouse-rabbit transmission barrier was used as a model. To identify which specific amino acid residues determine high or low susceptibility to PrPSc propagation, protein misfolding cyclic amplification (PMCA), which mimics PrPC-to-PrPSc conversion with accelerated kinetics, was used. This allowed amino acid substitutions in rabbit PrP and accurate analysis of misfolding propensities. Wild-type rabbit recombinant PrP could not be misfolded into a protease-resistant self-propagating isoform in vitro despite seeding with at least 12 different infectious prions from diverse origins. Therefore, rabbit recombinant PrP mutants were designed to contain every single amino acid substitution that distinguishes rabbit recombinant PrP from mouse recombinant PrP. Key amino acid residue substitutions were identified that make rabbit recombinant PrP susceptible to misfolding, and using these, protease-resistant misfolded recombinant rabbit PrP was generated. Additional studies characterized the mechanisms by which these critical amino acid residue substitutions increased the misfolding susceptibility of rabbit PrP.IMPORTANCE Prion disorders are invariably fatal, untreatable diseases typically associated with long incubation periods and characteristic spongiform changes associated with neuronal loss in the brain. Development of any treatment or preventative measure is dependent upon a detailed understanding of the pathogenesis of these diseases, and understanding the mechanism by which certain species appear to be resistant to TSEs is critical. Rabbits are highly resistant to naturally acquired TSEs, and even under experimental conditions, induction of clinical disease is not easy. Using recombinant rabbit PrP as a model, this study describes critical molecular determinants that confer this high resistance to transmissible spongiform encephalopathies.
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Ladner-Keay CL, LeVatte M, Wishart DS. Role of polysaccharide and lipid in lipopolysaccharide induced prion protein conversion. Prion 2017; 10:466-483. [PMID: 27906600 PMCID: PMC5161299 DOI: 10.1080/19336896.2016.1254857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Conversion of native cellular prion protein (PrPc) from an α-helical structure to a toxic and infectious β-sheet structure (PrPSc) is a critical step in the development of prion disease. There are some indications that the formation of PrPSc is preceded by a β-sheet rich PrP (PrPβ) form which is non-infectious, but is an intermediate in the formation of infectious PrPSc. Furthermore the presence of lipid cofactors is thought to be critical in the formation of both intermediate-PrPβ and lethal, infectious PrPSc. We previously discovered that the endotoxin, lipopolysaccharide (LPS), interacts with recombinant PrPc and induces rapid conformational change to a β-sheet rich structure. This LPS induced PrPβ structure exhibits PrPSc-like features including proteinase K (PK) resistance and the capacity to form large oligomers and rod-like fibrils. LPS is a large, complex molecule with lipid, polysaccharide, 2-keto-3-deoxyoctonate (Kdo) and glucosamine components. To learn more about which LPS chemical constituents are critical for binding PrPc and inducing β-sheet conversion we systematically investigated which chemical components of LPS either bind or induce PrP conversion to PrPβ. We analyzed this PrP conversion using resolution enhanced native acidic gel electrophoresis (RENAGE), tryptophan fluorescence, circular dichroism, electron microscopy and PK resistance. Our results indicate that a minimal version of LPS (called detoxified and partially de-acylated LPS or dLPS) containing a portion of the polysaccharide and a portion of the lipid component is sufficient for PrP conversion. Lipid components, alone, and saccharide components, alone, are insufficient for conversion.
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Affiliation(s)
- Carol L Ladner-Keay
- a Department of Biological Sciences , University of Alberta , Edmonton , Alberta , Canada
| | - Marcia LeVatte
- a Department of Biological Sciences , University of Alberta , Edmonton , Alberta , Canada
| | - David S Wishart
- a Department of Biological Sciences , University of Alberta , Edmonton , Alberta , Canada.,b Department of Computing Science , University of Alberta , Edmonton , Alberta , Canada
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40
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Ke PC, Sani MA, Ding F, Kakinen A, Javed I, Separovic F, Davis TP, Mezzenga R. Implications of peptide assemblies in amyloid diseases. Chem Soc Rev 2017; 46:6492-6531. [PMID: 28702523 PMCID: PMC5902192 DOI: 10.1039/c7cs00372b] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Neurodegenerative disorders and type 2 diabetes are global epidemics compromising the quality of life of millions worldwide, with profound social and economic implications. Despite the significant differences in pathology - much of which are poorly understood - these diseases are commonly characterized by the presence of cross-β amyloid fibrils as well as the loss of neuronal or pancreatic β-cells. In this review, we document research progress on the molecular and mesoscopic self-assembly of amyloid-beta, alpha synuclein, human islet amyloid polypeptide and prions, the peptides and proteins associated with Alzheimer's, Parkinson's, type 2 diabetes and prion diseases. In addition, we discuss the toxicities of these amyloid proteins based on their self-assembly as well as their interactions with membranes, metal ions, small molecules and engineered nanoparticles. Through this presentation we show the remarkable similarities and differences in the structural transitions of the amyloid proteins through primary and secondary nucleation, the common evolution from disordered monomers to alpha-helices and then to β-sheets when the proteins encounter the cell membrane, and, the consensus (with a few exceptions) that off-pathway oligomers, rather than amyloid fibrils, are the toxic species regardless of the pathogenic protein sequence or physicochemical properties. In addition, we highlight the crucial role of molecular self-assembly in eliciting the biological and pathological consequences of the amyloid proteins within the context of their cellular environments and their spreading between cells and organs. Exploiting such structure-function-toxicity relationship may prove pivotal for the detection and mitigation of amyloid diseases.
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Affiliation(s)
- Pu Chun Ke
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Marc-Antonie Sani
- School of Chemistry, Bio21 Institute, The University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Aleksandr Kakinen
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ibrahim Javed
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Thomas P. Davis
- ARC Center of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Raffaele Mezzenga
- ETH Zurich, Department of Health Science & Technology, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
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41
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Iwakawa N, Morimoto D, Walinda E, Kawata Y, Shirakawa M, Sugase K. Real-Time Observation of the Interaction between Thioflavin T and an Amyloid Protein by Using High-Sensitivity Rheo-NMR. Int J Mol Sci 2017; 18:ijms18112271. [PMID: 29143789 PMCID: PMC5713241 DOI: 10.3390/ijms18112271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 01/27/2023] Open
Abstract
Amyloid fibril formation is associated with numerous neurodegenerative diseases. To elucidate the mechanism of fibril formation, the thioflavin T (ThT) fluorescence assay is widely used. ThT is a fluorescent dye that selectively binds to amyloid fibrils and exhibits fluorescence enhancement, which enables quantitative analysis of the fibril formation process. However, the detailed binding mechanism has remained unclear. Here we acquire real-time profiles of fibril formation of superoxide dismutase 1 (SOD1) using high-sensitivity Rheo-NMR spectroscopy and detect weak and strong interactions between ThT and SOD1 fibrils in a time-dependent manner. Real-time information on the interaction between ThT and fibrils will contribute to the understanding of the binding mechanism of ThT to fibrils. In addition, our method provides an alternative way to analyze fibril formation.
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Affiliation(s)
- Naoto Iwakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-cho Minami, Tottori 680-8552, Japan.
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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42
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Legname G, Moda F. The Prion Concept and Synthetic Prions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 150:147-156. [PMID: 28838659 DOI: 10.1016/bs.pmbts.2017.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
Transmissible spongiform encephalopathies or prion diseases are a group of fatal neurodegenerative diseases caused by unconventional infectious agents, known as prions (PrPSc). Prions derive from a conformational conversion of the normally folded prion protein (PrPC), which acquires pathological and infectious features. Moreover, PrPSc is able to transmit the pathological conformation to PrPC through a mechanism that is still not well understood. The generation of synthetic prions, which behave like natural prions, is of fundamental importance to study the process of PrPC conversion and to assess the efficacy of therapeutic strategies to interfere with this process. Moreover, the ability of synthetic prions to induce pathology in animals confirms that the pathological properties of the prion strains are all enciphered in abnormal conformations, characterizing these infectious agents.
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Affiliation(s)
- Giuseppe Legname
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
| | - Fabio Moda
- IRCCS Foundation Carlo Besta Neurological Institute, Milan, Italy.
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43
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Sengupta I, Bhate SH, Das R, Udgaonkar JB. Salt-Mediated Oligomerization of the Mouse Prion Protein Monitored by Real-Time NMR. J Mol Biol 2017; 429:1852-1872. [DOI: 10.1016/j.jmb.2017.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 12/11/2022]
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44
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Adelizzi B, Filot IAW, Palmans ARA, Meijer EW. Unravelling the Pathway Complexity in Conformationally Flexible N-Centered Triarylamine Trisamides. Chemistry 2017; 23:6103-6110. [PMID: 27981630 PMCID: PMC5434799 DOI: 10.1002/chem.201603938] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 11/06/2022]
Abstract
Two families of C3 -symmetrical triarylamine-trisamides comprising a triphenylamine- or a tri(pyrid-2-yl)amine core are presented. Both families self-assemble in apolar solvents via cooperative hydrogen-bonding interactions into helical supramolecular polymers as evidenced by a combination of spectroscopic measurements, and corroborated by DFT calculations. The introduction of a stereocenter in the side chains biases the helical sense of the supramolecular polymers formed. Compared to other C3 -symmetrical compounds, a much richer self-assembly landscape is observed. Temperature-dependent spectroscopy measurements highlight the presence of two self-assembled states of opposite handedness. One state is formed at high temperature from a molecularly dissolved solution via a nucleation-elongation mechanism. The second state is formed below room temperature through a sharp transition from the first assembled state. The change in helicity is proposed to be related to a conformational switch of the triarylamine core due to an equilibrium between a 3:0 and a 2:1 conformation. Thus, within a limited temperature window, a small conformational twist results in an assembled state of opposite helicity.
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Affiliation(s)
- Beatrice Adelizzi
- Laboratory of Macromolecular and Organic ChemistryEindhoven University of TechnologyEindhovenThe Netherlands
- Institute for Complex Molecular SystemsEindhoven University of TechnologyEindhovenThe Netherlands
| | - Ivo A. W. Filot
- Institute of CatalysisEindhoven University of TechnologyEindhovenThe Netherlands
| | - Anja R. A. Palmans
- Laboratory of Macromolecular and Organic ChemistryEindhoven University of TechnologyEindhovenThe Netherlands
- Institute for Complex Molecular SystemsEindhoven University of TechnologyEindhovenThe Netherlands
| | - E. W. Meijer
- Laboratory of Macromolecular and Organic ChemistryEindhoven University of TechnologyEindhovenThe Netherlands
- Institute for Complex Molecular SystemsEindhoven University of TechnologyEindhovenThe Netherlands
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45
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Yamauchi M, Adhikari B, Prabhu DD, Lin X, Karatsu T, Ohba T, Shimizu N, Takagi H, Haruki R, Adachi SI, Kajitani T, Fukushima T, Yagai S. Supramolecular Polymerization of Supermacrocycles: Effect of Molecular Conformations on Kinetics and Morphology. Chemistry 2017; 23:5270-5280. [DOI: 10.1002/chem.201605873] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Mitsuaki Yamauchi
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Bimalendu Adhikari
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Deepak D. Prabhu
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Xu Lin
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Takashi Karatsu
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Tomonori Ohba
- Department of Chemistry, Graduate School of Science; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
| | - Nobutaka Shimizu
- Photon Factory, Institute of Materials Structure Science; High Energy Accelerator Research Organization; 1-1, Oho Tsukuba 305-0801 Japan
| | - Hideaki Takagi
- Photon Factory, Institute of Materials Structure Science; High Energy Accelerator Research Organization; 1-1, Oho Tsukuba 305-0801 Japan
| | - Rie Haruki
- Photon Factory, Institute of Materials Structure Science; High Energy Accelerator Research Organization; 1-1, Oho Tsukuba 305-0801 Japan
| | - Shin-ichi Adachi
- Photon Factory, Institute of Materials Structure Science; High Energy Accelerator Research Organization; 1-1, Oho Tsukuba 305-0801 Japan
| | - Takashi Kajitani
- Laboratory for Chemistry and Life Science, Institute of Innovative Research; Tokyo Institute of Technology; 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
- RIKEN SPring-8 Center; 1-1-1 Kouto, Sayo Hyogo 679-5148 Japan
| | - Takanori Fukushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research; Tokyo Institute of Technology; 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Shiki Yagai
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
- Molecular Chirality Research Center; Chiba University; 1-33 Yayoi-cho, Inage-ku Chiba 263-8522 Japan
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46
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Singh RK, Chamachi NG, Chakrabarty S, Mukherjee A. Mechanism of Unfolding of Human Prion Protein. J Phys Chem B 2017; 121:550-564. [PMID: 28030950 DOI: 10.1021/acs.jpcb.6b11416] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Misfolding and aggregation of prion proteins are associated with several neurodegenerative diseases. Therefore, understanding the mechanism of the misfolding process is of enormous interest in the scientific community. It has been speculated and widely discussed that the native cellular prion protein (PrPC) form needs to undergo substantial unfolding to a more stable PrPC* state, which may further oligomerize into the toxic scrapie (PrPSc) form. Here, we have studied the mechanism of the unfolding of the human prion protein (huPrP) using a set of extensive well-tempered metadynamics simulations. Through multiple microsecond-long metadynamics simulations, we find several possible unfolding pathways. We show that each pathway leads to an unfolded state of lower free energy than the native state. Thus, our study may point to the signature of a PrPC* form that corresponds to a global minimum on the conformational free-energy landscape. Moreover, we find that these global minima states do not involve an increased β-sheet content, as was assumed to be a signature of PrPSc formation in previous simulation studies. We have further analyzed the origin of metastability of the PrPC form through free-energy surfaces of the chopped helical segments to show that the helices, particularly H2 and H3 of the prion protein, have the tendency to form either a random coil or a β-structure. Therefore, the secondary structural elements of the prion protein are only weakly stabilized by tertiary contacts and solvation forces so that relatively weak perturbations induced by temperature, pressure, pH, and so forth can lead to substantial unfolding with characteristics of intrinsically disordered proteins.
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Affiliation(s)
- Reman K Singh
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
| | - Neharika G Chamachi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
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47
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Wang T, Wang R, Chen Z, Zhong Q. Magnetization of eugenol to fabricate magnetic-responsive emulsions for targeted delivery of caffeic acid phenethyl ester. RSC Adv 2017. [DOI: 10.1039/c7ra08167g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The manipulative colloidal vehicles with appreciable stability were fabricated by rice proteins under an eco-friendly, cross-linkage free environment, which can be tailored for targeted delivery of diagnostic or curative drugs.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology
| | - Ren Wang
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology
| | - Zhengxing Chen
- State Key Laboratory of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- People's Republic of China
- National Engineering Laboratory for Cereal Fermentation Technology
| | - Qixin Zhong
- Department of Food Science and Technology
- University of Tennessee
- Knoxville
- USA
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48
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Besenius P. Controlling supramolecular polymerization through multicomponent self-assembly. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/pola.28385] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Pol Besenius
- Institute of Organic Chemistry, Johannes Gutenberg-Universität Mainz; Duesbergweg 10-14 Mainz 55128 Germany
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49
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Ranganathan S, Maji SK, Padinhateeri R. Defining a Physical Basis for Diversity in Protein Self-Assemblies Using a Minimal Model. J Am Chem Soc 2016; 138:13911-13922. [DOI: 10.1021/jacs.6b06433] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Srivastav Ranganathan
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Samir K. Maji
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences
and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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50
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Yu Z, Huang P, Yu Y, Zheng Z, Huang Z, Guo C, Lin D. Unique Properties of the Rabbit Prion Protein Oligomer. PLoS One 2016; 11:e0160874. [PMID: 27529173 PMCID: PMC4987043 DOI: 10.1371/journal.pone.0160874] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 07/26/2016] [Indexed: 11/26/2022] Open
Abstract
Prion diseases, also known as transmissible spongiform encephalopathies (TSEs), are a group of fatal neurodegenerative disorders infecting both humans and animals. Recent works have demonstrated that the soluble prion protein oligomer (PrPO), the intermediate of the conformational transformation from the host-derived cellular form (PrPC) to the disease-associated Scrapie form (PrPSc), exerts the major neurotoxicity in vitro and in vivo. Rabbits show strong resistance to TSEs, the underlying mechanism is unclear to date. It is expected that the relative TSEs-resistance of rabbits is closely associated with the unique properties of rabbit prion protein oligomer which remain to be addressed in detail. In the present work, we prepared rabbit prion protein oligomer (recRaPrPO) and human prion protein oligomer (recHuPrPO) under varied conditions, analyzed the effects of pH, NaCl concentration and incubation temperature on the oligomerization, and compared the properties of recRaPrPO and recHuPrPO. We found that several factors facilitated the formation of prion protein oligomers, including low pH, high NaCl concentration, high incubation temperature and low conformational stability of monomeric prion protein. RecRaPrPO was formed more slowly than recHuPrPO at physiological-like conditions (< 57°C, < 150 mM NaCl). Furthermore, recRaPrPO possessed higher susceptibility to proteinase K and lower cytotoxicity in vitro than recHuPrPO. These unique properties of recRaPrPO might substantially contribute to the TSEs-resistance of rabbits. Our work sheds light on the oligomerization of prion proteins and is of benefit to mechanistic understanding of TSEs-resistance of rabbits.
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Affiliation(s)
- Ziyao Yu
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Pei Huang
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuanhui Yu
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhen Zheng
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zicheng Huang
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chenyun Guo
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- The Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- * E-mail:
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