1
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Aissaoui N, Mills A, Lai-Kee-Him J, Triomphe N, Cece Q, Doucet C, Bonhoure A, Vidal M, Ke Y, Bellot G. Free-Standing DNA Origami Superlattice to Facilitate Cryo-EM Visualization of Membrane Vesicles. J Am Chem Soc 2024; 146:12925-12932. [PMID: 38691507 DOI: 10.1021/jacs.3c07328] [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: 05/03/2024]
Abstract
Technological breakthroughs in cryo-electron microscopy (cryo-EM) methods open new perspectives for highly detailed structural characterizations of extracellular vesicles (EVs) and synthetic liposome-protein assemblies. Structural characterizations of these vesicles in solution under a nearly native hydrated state are of great importance to decipher cell-to-cell communication and to improve EVs' application as markers in diagnosis and as drug carriers in disease therapy. However, difficulties in preparing holey carbon cryo-EM grids with low vesicle heterogeneities, at low concentration and with kinetic control of the chemical reactions or assembly processes, have limited cryo-EM use in the EV study. We report a straightforward membrane vesicle cryo-EM sample preparation method that assists in circumventing these limitations by using a free-standing DNA-affinity superlattice for covering holey carbon cryo-EM grids. Our approach uses DNA origami to self-assemble to a solution-stable and micrometer-sized ordered molecular template in which structure and functional properties can be rationally controlled. We engineered the template with cholesterol-binding sites to specifically trap membrane vesicles. The advantages of this DNA-cholesterol-affinity lattice (DCAL) include (1) local enrichment of artificial and biological vesicles at low concentration and (2) isolation of heterogeneous cell-derived membrane vesicles (exosomes) from a prepurified pellet of cell culture conditioned medium on the grid.
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Affiliation(s)
| | - Allan Mills
- Université de Montpellier, CNRS, INSERM, Centre de Biologie Structurale, F-34000 Montpellier, France
| | - Josephine Lai-Kee-Him
- Université de Montpellier, CNRS, INSERM, Centre de Biologie Structurale, F-34000 Montpellier, France
| | - Nicolas Triomphe
- Université de Montpellier, CNRS, INSERM, Centre de Biologie Structurale, F-34000 Montpellier, France
| | - Quentin Cece
- Université Paris Cité, CNRS, CiTCoM, F-75006 Paris, France
| | - Christine Doucet
- Université de Montpellier, CNRS, INSERM, Centre de Biologie Structurale, F-34000 Montpellier, France
| | - Anne Bonhoure
- Université de Montpellier, CNRS, LPHI, F-34000 Montpellier, France
| | - Michel Vidal
- Université de Montpellier, CNRS, LPHI, F-34000 Montpellier, France
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 30322 Atlanta, United States
| | - Gaetan Bellot
- Université de Montpellier, CNRS, INSERM, Centre de Biologie Structurale, F-34000 Montpellier, France
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2
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Xing H, Wigham C, Lee SR, Pereira AJ, de Campos LJ, Picco AS, Huck-Iriart C, Escudero C, Perez-Chirinos L, Gajaweera S, Comer J, Sasselli IR, Stupp SI, Zha RH, Conda-Sheridan M. Enhanced Hydrogen Bonding by Urea Functionalization Tunes the Stability and Biological Properties of Peptide Amphiphiles. Biomacromolecules 2024; 25:2823-2837. [PMID: 38602228 DOI: 10.1021/acs.biomac.3c01463] [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: 04/12/2024]
Abstract
Self-assembled nanostructures such as those formed by peptide amphiphiles (PAs) are of great interest in biological and pharmacological applications. Herein, a simple and widely applicable chemical modification, a urea motif, was included in the PA's molecular structure to stabilize the nanostructures by virtue of intermolecular hydrogen bonds. Since the amino acid residue nearest to the lipid tail is the most relevant for stability, we decided to include the urea modification at that position. We prepared four groups of molecules (13 PAs in all), with varying levels of intermolecular cohesion, using amino acids with distinct β-sheet promoting potential and/or containing hydrophobic tails of distinct lengths. Each subset contained one urea-modified PA and nonmodified PAs, all with the same peptide sequence. The varied responses of these PAs to variations in pH, temperature, counterions, and biologically related proteins were examined using microscopic, X-ray, spectrometric techniques, and molecular simulations. We found that the urea group contributes to the stabilization of the morphology and internal arrangement of the assemblies against environmental stimuli for all peptide sequences. In addition, microbiological and biological studies were performed with the cationic PAs. These assays reveal that the addition of urea linkages affects the PA-cell membrane interaction, showing the potential to increase the selectivity toward bacteria. Our data indicate that the urea motif can be used to tune the stability of a wide range of PA nanostructures, allowing flexibility on the biomaterial's design and opening a myriad of options for clinical therapies.
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Affiliation(s)
- Huihua Xing
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Caleb Wigham
- Department of Chemical & Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Sieun Ruth Lee
- Department of Materials Science & Engineering, Chemistry, Biomedical Engineering, Medicine, and Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Aramis J Pereira
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Luana J de Campos
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Agustín S Picco
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, INIFTA-CONICET-UNLP, La Plata 1900, Argentina
| | - Cristián Huck-Iriart
- ALBA Synchrotron Light Source, Experiments Division, 08290 Cerdanyola del Vallès, Spain
| | - Carlos Escudero
- ALBA Synchrotron Light Source, Experiments Division, 08290 Cerdanyola del Vallès, Spain
| | - Laura Perez-Chirinos
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia 20014, San Sebastián, Spain
| | - Sandun Gajaweera
- Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506, United States
| | - Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ivan R Sasselli
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia 20014, San Sebastián, Spain
- Centro de Fisica de Materiales (CFM), CSIC-UPV/EHU, Donostia 20018, San Sebastián, Spain
| | - Samuel I Stupp
- Department of Materials Science & Engineering, Chemistry, Biomedical Engineering, Medicine, and Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - R Helen Zha
- Department of Chemical & Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Martin Conda-Sheridan
- College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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3
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Kinger S, Jagtap YA, Kumar P, Choudhary A, Prasad A, Prajapati VK, Kumar A, Mehta G, Mishra A. Proteostasis in neurodegenerative diseases. Adv Clin Chem 2024; 121:270-333. [PMID: 38797543 DOI: 10.1016/bs.acc.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Proteostasis is essential for normal function of proteins and vital for cellular health and survival. Proteostasis encompasses all stages in the "life" of a protein, that is, from translation to functional performance and, ultimately, to degradation. Proteins need native conformations for function and in the presence of multiple types of stress, their misfolding and aggregation can occur. A coordinated network of proteins is at the core of proteostasis in cells. Among these, chaperones are required for maintaining the integrity of protein conformations by preventing misfolding and aggregation and guide those with abnormal conformation to degradation. The ubiquitin-proteasome system (UPS) and autophagy are major cellular pathways for degrading proteins. Although failure or decreased functioning of components of this network can lead to proteotoxicity and disease, like neuron degenerative diseases, underlying factors are not completely understood. Accumulating misfolded and aggregated proteins are considered major pathomechanisms of neurodegeneration. In this chapter, we have described the components of three major branches required for proteostasis-chaperones, UPS and autophagy, the mechanistic basis of their function, and their potential for protection against various neurodegenerative conditions, like Alzheimer's, Parkinson's, and Huntington's disease. The modulation of various proteostasis network proteins, like chaperones, E3 ubiquitin ligases, proteasome, and autophagy-associated proteins as therapeutic targets by small molecules as well as new and unconventional approaches, shows promise.
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Affiliation(s)
- Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, India
| | - Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India.
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4
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Gigon L, Müller P, Haenni B, Iacovache I, Barbo M, Gosheva G, Yousefi S, Soragni A, von Ballmoos C, Zuber B, Simon HU. Membrane damage by MBP-1 is mediated by pore formation and amplified by mtDNA. Cell Rep 2024; 43:114084. [PMID: 38583154 DOI: 10.1016/j.celrep.2024.114084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/28/2023] [Accepted: 03/25/2024] [Indexed: 04/09/2024] Open
Abstract
Eosinophils play a crucial role in host defense while also contributing to immunopathology through the release of inflammatory mediators. Characterized by distinctive cytoplasmic granules, eosinophils securely store and rapidly release various proteins exhibiting high toxicity upon extracellular release. Among these, major basic protein 1 (MBP-1) emerges as an important mediator in eosinophil function against pathogens and in eosinophil-associated diseases. While MBP-1 targets both microorganisms and host cells, its precise mechanism remains elusive. We demonstrate that formation of small pores by MBP-1 in lipid bilayers induces membrane permeabilization and disrupts potassium balance. Additionally, we reveal that mitochondrial DNA (mtDNA) present in eosinophil extracellular traps (EETs) amplifies MBP-1 toxic effects, underscoring the pivotal role of mtDNA in EETs. Furthermore, we present evidence indicating that absence of CpG methylation in mtDNA contributes to the regulation of MBP-1-mediated toxicity. Taken together, our data suggest that the mtDNA scaffold within extracellular traps promotes MBP-1 toxicity.
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Affiliation(s)
- Lea Gigon
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland
| | - Philipp Müller
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Beat Haenni
- Institute of Anatomy, University of Bern, 3012 Bern, Switzerland
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern, 3012 Bern, Switzerland
| | - Maruša Barbo
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland; Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Gordana Gosheva
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland; Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Shida Yousefi
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland
| | - Alice Soragni
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christoph von Ballmoos
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, 3012 Bern, Switzerland
| | - Hans-Uwe Simon
- Institute of Pharmacology, University of Bern, 3010 Bern, Switzerland; Institute of Biochemistry, Brandenburg Medical School, 16816 Neuruppin, Germany.
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5
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Zhang R, Jalali S, Dias CL, Haataja MP. Growth kinetics of amyloid-like fibrils: An integrated atomistic simulation and continuum theory approach. PNAS NEXUS 2024; 3:pgae045. [PMID: 38725528 PMCID: PMC11079572 DOI: 10.1093/pnasnexus/pgae045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/19/2024] [Indexed: 05/12/2024]
Abstract
Amyloid fibrils have long been associated with many neurodegenerative diseases. The conventional picture of the formation and proliferation of fibrils from unfolded proteins comprises primary and secondary nucleation of oligomers followed by elongation and fragmentation thereof. In this work, we first employ extensive all-atom molecular dynamics (MD) simulations of short peptides to investigate the governing processes of fibril growth at the molecular scale. We observe that the peptides in the bulk solution can bind onto and subsequently diffuse along the fibril surface, which leads to fibril elongation via either bulk- or surface-mediated docking mechanisms. Then, to guide the quantitative interpretation of these observations and to provide a more comprehensive picture of the growth kinetics of single fibrils, a continuum model which incorporates the key processes observed in the MD simulations is formulated. The model is employed to investigate how relevant physical parameters affect the kinetics of fibril growth and identify distinct growth regimes. In particular, it is shown that fibrils which strongly bind peptides may undergo a transient exponential growth phase in which the entire fibril surface effectively acts as a sink for peptides. We also demonstrate how the relevant model parameters can be estimated from the MD trajectories. Our results provide compelling evidence that the overall fibril growth rates are determined by both bulk and surface peptide fluxes, thereby contributing to a more fundamental understanding of the growth kinetics of amyloid-like fibrils.
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Affiliation(s)
- Ruoyao Zhang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Cristiano Luis Dias
- Department of Physics, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Mikko P Haataja
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
- Princeton Materials Institute, Princeton University, Princeton, NJ 08544, USA
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6
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De Luca A, Faienza F, Fulci C, Nicolai E, Calligari P, Palumbo C, Caccuri AM. Molecular and cellular evidence of a direct interaction between the TRAF2 C-terminal domain and ganglioside GM1. Int J Biochem Cell Biol 2024; 167:106508. [PMID: 38142771 DOI: 10.1016/j.biocel.2023.106508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/30/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
TNF receptor-associated factor 2 (TRAF2) is involved in different cellular processes including signal transduction and transcription regulation. We here provide evidence of a direct interaction between the TRAF domain of TRAF2 and the monosialotetrahexosylganglioside (GM1). Previously, we showed that the TRAF domain occurs mainly in a trimeric form in solution, but it can also exist as a stable monomer when in the nanomolar concentration range. Here, we report that the quaternary structure of the TRAF domain is also affected by pH changes, since a weakly acidic pH (5.5) favors the dissociation of the trimeric TRAF domain into stable monomers, as previously observed at neutral pH (7.6) with the diluted protein. The TRAF domain-GM1 binding was similar at pH 5.5 and 7.6, suggesting that GM1 interacts with both the trimeric and monomeric forms of the protein. However, only the monomeric protein appeared to cause membrane deformation and inward vesiculation in GM1-containing giant unilamellar vesicles (GUVs). The formation of complexes between GM1 and TRAF2, or its TRAF domain, was also observed in cultured human leukemic HAP1 cells expressing either the truncated TRAF domain or the endogenous full length TRAF2. The GM1-protein complexes were observed after treatment with tunicamycin and were more concentrated in cells undergoing apoptosis, a condition which is known to cause cytoplasm acidification. These findings open the avenue for future studies aimed at deciphering the physiopathological relevance of the TRAF domain-GM1 interaction.
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Affiliation(s)
| | - Fiorella Faienza
- Department of Chemical Sciences and Technologies, University of Tor Vergata, Rome, Italy
| | - Chiara Fulci
- Department of Chemical Sciences and Technologies, University of Tor Vergata, Rome, Italy
| | - Eleonora Nicolai
- Department of Experimental Medicine, University of Tor Vergata, Rome, Italy
| | - Paolo Calligari
- Department of Chemical Sciences and Technologies, University of Tor Vergata, Rome, Italy
| | - Camilla Palumbo
- Department of Clinical Sciences and Translational Medicine, University of Tor Vergata, Rome, Italy.
| | - Anna Maria Caccuri
- Department of Chemical Sciences and Technologies, University of Tor Vergata, Rome, Italy; The NAST Centre for Nanoscience and Nanotechnology and Innovative Instrumentation, University of Tor Vergata, Rome, Italy.
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7
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Regmi D, Shen F, Stanic A, Islam M, Du D. Effect of phospholipid liposomes on prion fragment (106-128) amyloid formation. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184199. [PMID: 37454869 DOI: 10.1016/j.bbamem.2023.184199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/08/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Misfolding and aggregation of cellular prion protein (PrPc) is a major molecular process involved in the pathogenesis of prion diseases. Here, we studied the aggregation properties of a prion fragment peptide PrP(106-128). The results show that the peptide aggregates in a concentration-dependent manner in an aqueous solution and that the aggregation is sensitive to pH and the preformed amyloid seeds. Furthermore, we show that the zwitterionic POPC liposomes moderately inhibit the aggregation of PrP(106-128), whereas POPC/cholesterol (8:2) vesicles facilitate peptide aggregation likely due to the increase of the lipid packing order and membrane rigidity in the presence of cholesterol. In addition, anionic lipid vesicles of POPG and POPG/cholesterol above a certain concentration accelerate the aggregation of the peptide remarkably. The strong electrostatic interactions between the N-terminal region of the peptide and POPG may constrain the conformational plasticity of the peptide, preventing insertion of the peptide into the inner side of the membrane and thus promoting fibrillation on the membrane surface. The results suggest that the charge properties of the membrane, the composition of the liposomes, and the rigidity of lipid packing are critical in determining peptide adsorption on the membrane surface and the efficiency of the membrane in catalyzing peptide oligomeric nucleation and amyloid formation. The peptide could be used as an improved model molecule to investigate the mechanistic role of the crucial regions of PrP in aggregation in a membrane-rich environment and to screen effective inhibitors to block key interactions between these regions and membranes for preventing PrP aggregation.
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Affiliation(s)
- Deepika Regmi
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Aleksander Stanic
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Majedul Islam
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA.
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8
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Jana B, Jin S, Go EM, Cho Y, Kim D, Kim S, Kwak SK, Ryu JH. Intra-Lysosomal Peptide Assembly for the High Selectivity Index against Cancer. J Am Chem Soc 2023; 145:18414-18431. [PMID: 37525328 DOI: 10.1021/jacs.3c04467] [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: 08/02/2023]
Abstract
Lysosomes remain powerful organelles and important targets for cancer therapy because cancer cell proliferation is greatly dependent on effective lysosomal function. Recent studies have shown that lysosomal membrane permeabilization induces cell death and is an effective way to treat cancer by bypassing the classical caspase-dependent apoptotic pathway. However, most lysosome-targeted anticancer drugs have very low selectivity for cancer cells. Here, we show intra-lysosomal self-assembly of a peptide amphiphile as a powerful technique to overcome this problem. We designed a peptide amphiphile that localizes in the cancer lysosome and undergoes cathepsin B enzyme-instructed supramolecular assembly. This localized assembly induces lysosomal swelling, membrane permeabilization, and damage to the lysosome, which eventually causes caspase-independent apoptotic death of cancer cells without conventional chemotherapeutic drugs. It has specific anticancer effects and is effective against drug-resistant cancers. Moreover, this peptide amphiphile exhibits high tumor targeting when attached to a tumor-targeting ligand and causes significant inhibition of tumor growth both in cancer and drug-resistant cancer xenograft models.
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Affiliation(s)
- Batakrishna Jana
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seongeon Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Eun Min Go
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yumi Cho
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dohyun Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sangpil Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sang Kyu Kwak
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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9
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Kaygisiz K, Rauch-Wirth L, Dutta A, Yu X, Nagata Y, Bereau T, Münch J, Synatschke CV, Weil T. Data-mining unveils structure-property-activity correlation of viral infectivity enhancing self-assembling peptides. Nat Commun 2023; 14:5121. [PMID: 37612273 PMCID: PMC10447463 DOI: 10.1038/s41467-023-40663-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
Gene therapy via retroviral vectors holds great promise for treating a variety of serious diseases. It requires the use of additives to boost infectivity. Amyloid-like peptide nanofibers (PNFs) were shown to efficiently enhance retroviral gene transfer. However, the underlying mode of action of these peptides remains largely unknown. Data-mining is an efficient method to systematically study structure-function relationship and unveil patterns in a database. This data-mining study elucidates the multi-scale structure-property-activity relationship of transduction enhancing peptides for retroviral gene transfer. In contrast to previous reports, we find that not the amyloid fibrils themselves, but rather µm-sized β-sheet rich aggregates enhance infectivity. Specifically, microscopic aggregation of β-sheet rich amyloid structures with a hydrophobic surface pattern and positive surface charge are identified as key material properties. We validate the reliability of the amphiphilic sequence pattern and the general applicability of the key properties by rationally creating new active sequences and identifying short amyloidal peptides from various pathogenic and functional origin. Data-mining-even for small datasets-enables the development of new efficient retroviral transduction enhancers and provides important insights into the diverse bioactivity of the functional material class of amyloids.
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Affiliation(s)
- Kübra Kaygisiz
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Lena Rauch-Wirth
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Arghya Dutta
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany
| | - Xiaoqing Yu
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Yuki Nagata
- Department Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tristan Bereau
- Department Polymer Theory, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Meyerhofstraße 1, 89081, Ulm, Germany
| | - Christopher V Synatschke
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
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10
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202215785. [PMID: 38515735 PMCID: PMC10952214 DOI: 10.1002/ange.202215785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Indexed: 03/08/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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11
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Viles JH. Imaging Amyloid-β Membrane Interactions: Ion-Channel Pores and Lipid-Bilayer Permeability in Alzheimer's Disease. Angew Chem Int Ed Engl 2023; 62:e202215785. [PMID: 36876912 PMCID: PMC10953358 DOI: 10.1002/anie.202215785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/07/2023]
Abstract
The accumulation of the amyloid-β peptides (Aβ) is central to the development of Alzheimer's disease. The mechanism by which Aβ triggers a cascade of events that leads to dementia is a topic of intense investigation. Aβ self-associates into a series of complex assemblies with different structural and biophysical properties. It is the interaction of these oligomeric, protofibril and fibrillar assemblies with lipid membranes, or with membrane receptors, that results in membrane permeability and loss of cellular homeostasis, a key event in Alzheimer's disease pathology. Aβ can have an array of impacts on lipid membranes, reports have included: a carpeting effect; a detergent effect; and Aβ ion-channel pore formation. Recent advances imaging these interactions are providing a clearer picture of Aβ induced membrane disruption. Understanding the relationship between different Aβ structures and membrane permeability will inform therapeutics targeting Aβ cytotoxicity.
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Affiliation(s)
- John H. Viles
- Department of Biochemistry, SBBS, Queen MaryUniversity of LondonUK
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12
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Nguyen PH, Derreumaux P. An S-Shaped Aβ42 Cross-β Hexamer Embedded into a Lipid Bilayer Reveals Membrane Disruption and Permeability. ACS Chem Neurosci 2023; 14:936-946. [PMID: 36757886 DOI: 10.1021/acschemneuro.2c00785] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The interactions of amyloid oligomers with membranes are known to contribute to cellular toxicity. Numerous in vitro experimental studies reported on the insertion of oligomers of different sizes that can induce cell membrane disruption, extract lipids, and form ion-permeable transmembrane pores. The current repertoire of amyloid-beta (Aβ) membrane-inserted folds that was subject to high-resolution structure NMR spectroscopy and computer simulations is devoid of any cross-β fibrillar structure. In this study, we explored the dynamics of an S-shaped Aβ42 cross-β hexamer model inserted into a lipid bilayer membrane by two atomistic molecular dynamics simulations. The initial model is characterized by the hydrophobic residues at the central hydrophobic core (residues 17-21, CHC) and the C-terminus (residues 30-42) embedded into the membrane. We observed major structural secondary, tertiary, and quaternary rearrangements leading to two distinct species, hexamer and two trimers, accompanied by membrane disruption and water permeation. The simulations show that some configurations, but not the majority, have the CHC and C-terminus hydrophobic residues exposed to the solvent. Overall, our computational results offer new perspectives to understand the relationship between Aβ42 assemblies and membrane permeability.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Fondation Edmond de Rothschild, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Fondation Edmond de Rothschild, Université Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.,Institut Universitaire de France (IUF), 75005 Paris, France
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13
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Sohrabi T, Mirzaei-Behbahani B, Zadali R, Pirhaghi M, Morozova-Roche LA, Meratan AA. Common Mechanisms Underlying α-Synuclein-Induced Mitochondrial Dysfunction in Parkinson's Disease. J Mol Biol 2023:167992. [PMID: 36736886 DOI: 10.1016/j.jmb.2023.167992] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Parkinson's disease (PD) is the most common neurological movement disorder characterized by the selective and irreversible loss of dopaminergic neurons in substantia nigra pars compacta resulting in dopamine deficiency in the striatum. While most cases are sporadic or environmental, about 10% of patients have a positive family history with a genetic cause. The misfolding and aggregation of α-synuclein (α-syn) as a casual factor in the pathogenesis of PD has been supported by a great deal of literature. Extensive studies of mechanisms underpinning degeneration of the dopaminergic neurons induced by α-syn dysfunction suggest a complex process that involves multiple pathways, including mitochondrial dysfunction and increased oxidative stress, impaired calcium homeostasis through membrane permeabilization, synaptic dysfunction, impairment of quality control systems, disruption of microtubule dynamics and axonal transport, endoplasmic reticulum/Golgi dysfunction, nucleus malfunction, and microglia activation leading to neuroinflammation. Among them mitochondrial dysfunction has been considered as the most primary target of α-syn-induced toxicity, leading to neuronal cell death in both sporadic and familial forms of PD. Despite reviewing many aspects of PD pathogenesis related to mitochondrial dysfunction, a systemic study on how α-syn malfunction/aggregation damages mitochondrial functionality and leads to neurodegeneration is missing in the literature. In this review, we give a detailed molecular overview of the proposed mechanisms by which α-syn, directly or indirectly, contributes to mitochondrial dysfunction. This may provide valuable insights for development of new therapeutic approaches in relation to PD. Antioxidant-based therapy as a potential strategy to protect mitochondria against oxidative damage, its challenges, and recent developments in the field are discussed.
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Affiliation(s)
- Tahereh Sohrabi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Behnaz Mirzaei-Behbahani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Ramin Zadali
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Mitra Pirhaghi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Meratan
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
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14
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Zhang X, Lin L, Li H, Xia W, Liu Q, Zhou X, Dong L, Fu X. Update on new trend and progress of the mechanism of polysaccharides in the intervention of Alzheimer's disease, based on the new understanding of relevant theories: A review. Int J Biol Macromol 2022; 218:720-738. [PMID: 35902016 DOI: 10.1016/j.ijbiomac.2022.07.158] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 11/05/2022]
Abstract
Alzheimer's disease (AD), a neurodegenerative disease with insidious onset and progressive progression, is the main type of dementia. Currently, there is no specific cure for the disease. At the same time, a series of drug developments based on the classic theory, the Aβ cascade hypothesis, have not completed phase III clinical trials, challenging the hypothesis. Polysaccharides obtained from natural products can be used in the treatment of AD, which has attracted academic attention due to its advantages of multi-target, multi-channel, no or modest side effects. The TCM syndrome type of AD is mainly "qi and blood deficiency, kidney essence deficiency", and the medicine is mainly used to replenish qi and blood, kidney and bone marrow. Thus, there has been extensive and in-depth research on polysaccharides obtained from tonic Chinese herbal medicine in China. Based on this background, this paper evaluated the effects and mechanisms of natural polysaccharides on AD by combing and screening English and related literature in recent 5 years and summarized the extraction process and structure-activity relationship of polysaccharides.
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Affiliation(s)
- Xiaojing Zhang
- Ningxia Medical University, Yinchuan, 750004, China; General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Lizhen Lin
- Ningxia Medical University, Yinchuan, 750004, China
| | - Hang Li
- Ningxia Medical University, Yinchuan, 750004, China
| | - Wenxin Xia
- Ningxia Medical University, Yinchuan, 750004, China
| | - Qiansong Liu
- Ningxia Medical University, Yinchuan, 750004, China
| | - Xirong Zhou
- Ningxia Medical University, Yinchuan, 750004, China
| | - Lin Dong
- Ningxia Medical University, Yinchuan, 750004, China
| | - Xueyan Fu
- Ningxia Medical University, Yinchuan, 750004, China; Key Laboratory of Ningxia Minority Medicine Modernization, Ministry of Education (Ningxia Medical University), Yinchuan 750004, China.
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15
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Dicke SS, Maj M, Fields CR, Zanni MT. Metastable intermediate during hIAPP aggregation catalyzed by membranes as detected with 2D IR spectroscopy. RSC Chem Biol 2022; 3:931-940. [PMID: 35866164 PMCID: PMC9257649 DOI: 10.1039/d2cb00028h] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022] Open
Abstract
The aggregation of human islet amyloid polypeptide (hIAPP) into amyloid fibrils involves formation of oligomeric intermediates that are thought to be the cytotoxic species responsible for β-cell dysfunction in type 2 diabetes. hIAPP oligomers permeating or disrupting the cellular membrane may be one mechanism of toxicity and so measuring the structural kinetics of aggregation in the presence of membranes is of much interest. In this study, we use 2D IR spectroscopy and 13C18O isotope labeling to study the secondary structure of the oligomeric intermediates formed in solution and in the presence of phospholipid vesicles at sites L12A13, L16V17, G24A25 and V32G33. Pairs of labels monitor the couplings between associated polypeptides and the dihedral angles between adjacent residues. In solution, the L12A13 residues form an oligomeric β-sheet in addition to an α-helix whereas with the phospholipid vesicles they are α-helical throughout the aggregation process. In both solution and with DOPC vesicles, L16V17 and V32G33 have disordered structures until fibrils are formed. Similarly, under both conditions, G24A25 exhibits 3-state kinetics, created by an oligomeric intermediate with a well-defined β-sheet structure. Amyloid fibril formation is often thought to involve intermediates with exceedingly low populations that are difficult to detect experimentally. These experiments establish that amyloid fibril formation of hIAPP when catalyzed by membranes includes a metastable intermediate and that this intermediate has a similar structure at G24A25 in the FGAIL region as the corresponding intermediate in solution, thought to be the toxic species. 2D IR and 13C18O isotope labeling establish that amyloid formation of hIAPP catalyzed by membranes includes a metastable intermediate with a similar structure at G24A25 in the FGAIL region as the corresponding intermediate in solution.![]()
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Affiliation(s)
- Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Michał Maj
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA .,Formally at Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
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16
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Taylor AIP, Staniforth RA. General Principles Underpinning Amyloid Structure. Front Neurosci 2022; 16:878869. [PMID: 35720732 PMCID: PMC9201691 DOI: 10.3389/fnins.2022.878869] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Amyloid fibrils are a pathologically and functionally relevant state of protein folding, which is generally accessible to polypeptide chains and differs fundamentally from the globular state in terms of molecular symmetry, long-range conformational order, and supramolecular scale. Although amyloid structures are challenging to study, recent developments in techniques such as cryo-EM, solid-state NMR, and AFM have led to an explosion of information about the molecular and supramolecular organization of these assemblies. With these rapid advances, it is now possible to assess the prevalence and significance of proposed general structural features in the context of a diverse body of high-resolution models, and develop a unified view of the principles that control amyloid formation and give rise to their unique properties. Here, we show that, despite system-specific differences, there is a remarkable degree of commonality in both the structural motifs that amyloids adopt and the underlying principles responsible for them. We argue that the inherent geometric differences between amyloids and globular proteins shift the balance of stabilizing forces, predisposing amyloids to distinct molecular interaction motifs with a particular tendency for massive, lattice-like networks of mutually supporting interactions. This general property unites previously characterized structural features such as steric and polar zippers, and contributes to the long-range molecular order that gives amyloids many of their unique properties. The shared features of amyloid structures support the existence of shared structure-activity principles that explain their self-assembly, function, and pathogenesis, and instill hope in efforts to develop broad-spectrum modifiers of amyloid function and pathology.
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17
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Li D, Liu C. Conformational strains of pathogenic amyloid proteins in neurodegenerative diseases. Nat Rev Neurosci 2022; 23:523-534. [DOI: 10.1038/s41583-022-00603-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2022] [Indexed: 12/11/2022]
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18
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Tempra C, Scollo F, Pannuzzo M, Lolicato F, La Rosa C. A unifying framework for amyloid-mediated membrane damage: The lipid-chaperone hypothesis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140767. [PMID: 35144022 DOI: 10.1016/j.bbapap.2022.140767] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Over the past thirty years, researchers have highlighted the role played by a class of proteins or polypeptides that forms pathogenic amyloid aggregates in vivo, including i) the amyloid Aβ peptide, which is known to form senile plaques in Alzheimer's disease; ii) α-synuclein, responsible for Lewy body formation in Parkinson's disease and iii) IAPP, which is the protein component of type 2 diabetes-associated islet amyloids. These proteins, known as intrinsically disordered proteins (IDPs), are present as highly dynamic conformational ensembles. IDPs can partially (mis) fold into (dys) functional conformations and accumulate as amyloid aggregates upon interaction with other cytosolic partners such as proteins or lipid membranes. In addition, an increasing number of reports link the toxicity of amyloid proteins to their harmful effects on membrane integrity. Still, the molecular mechanism underlying the amyloidogenic proteins transfer from the aqueous environment to the hydrocarbon core of the membrane is poorly understood. This review starts with a historical overview of the toxicity models of amyloidogenic proteins to contextualize the more recent lipid-chaperone hypothesis. Then, we report the early molecular-level events in the aggregation and ion-channel pore formation of Aβ, IAPP, and α-synuclein interacting with model membranes, emphasizing the complexity of these processes due to their different spatial-temporal resolutions. Next, we underline the need for a combined experimental and computational approach, focusing on the strengths and weaknesses of the most commonly used techniques. Finally, the last two chapters highlight the crucial role of lipid-protein complexes as molecular switches among ion-channel-like formation, detergent-like, and fibril formation mechanisms and their implication in fighting amyloidogenic diseases.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
| | - Federica Scollo
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Pannuzzo
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
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19
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Kell DB, Laubscher GJ, Pretorius E. A central role for amyloid fibrin microclots in long COVID/PASC: origins and therapeutic implications. Biochem J 2022; 479:537-559. [PMID: 35195253 PMCID: PMC8883497 DOI: 10.1042/bcj20220016] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
Abstract
Post-acute sequelae of COVID (PASC), usually referred to as 'Long COVID' (a phenotype of COVID-19), is a relatively frequent consequence of SARS-CoV-2 infection, in which symptoms such as breathlessness, fatigue, 'brain fog', tissue damage, inflammation, and coagulopathies (dysfunctions of the blood coagulation system) persist long after the initial infection. It bears similarities to other post-viral syndromes, and to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Many regulatory health bodies still do not recognize this syndrome as a separate disease entity, and refer to it under the broad terminology of 'COVID', although its demographics are quite different from those of acute COVID-19. A few years ago, we discovered that fibrinogen in blood can clot into an anomalous 'amyloid' form of fibrin that (like other β-rich amyloids and prions) is relatively resistant to proteolysis (fibrinolysis). The result, as is strongly manifested in platelet-poor plasma (PPP) of individuals with Long COVID, is extensive fibrin amyloid microclots that can persist, can entrap other proteins, and that may lead to the production of various autoantibodies. These microclots are more-or-less easily measured in PPP with the stain thioflavin T and a simple fluorescence microscope. Although the symptoms of Long COVID are multifarious, we here argue that the ability of these fibrin amyloid microclots (fibrinaloids) to block up capillaries, and thus to limit the passage of red blood cells and hence O2 exchange, can actually underpin the majority of these symptoms. Consistent with this, in a preliminary report, it has been shown that suitable and closely monitored 'triple' anticoagulant therapy that leads to the removal of the microclots also removes the other symptoms. Fibrin amyloid microclots represent a novel and potentially important target for both the understanding and treatment of Long COVID and related disorders.
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, U.K
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kemitorvet 200, 2800 Kgs Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, South Africa
| | | | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch Private Bag X1 Matieland, 7602, South Africa
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20
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Low KJY, Venkatraman A, Mehta JS, Pervushin K. Molecular mechanisms of amyloid disaggregation. J Adv Res 2022; 36:113-132. [PMID: 35127169 PMCID: PMC8799873 DOI: 10.1016/j.jare.2021.05.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/13/2021] [Accepted: 05/16/2021] [Indexed: 12/17/2022] Open
Abstract
Importance of disaggregation mechanism and innate disaggregation in living systems. Different types and mechanism of disaggregation reported in literature. Structural details of the interactions and the disaggregation mechanisms. Amyloid disaggregation in protein aggregation disorders as a potential treatment. Proposed amyloid disaggregation mechanism of an ATP-independent chaperone (L-PGDS).
Introduction Protein aggregation and deposition of uniformly arranged amyloid fibrils in the form of plaques or amorphous aggregates is characteristic of amyloid diseases. The accumulation and deposition of proteins result in toxicity and cause deleterious effects on affected individuals known as amyloidosis. There are about fifty different proteins and peptides involved in amyloidosis including neurodegenerative diseases and diseases affecting vital organs. Despite the strenuous effort to find a suitable treatment option for these amyloid disorders, very few compounds had made it to unsuccessful clinical trials. It has become a compelling challenge to understand and manage amyloidosis with the increased life expectancy and ageing population. Objective While most of the currently available literature and knowledge base focus on the amyloid inhibitory mechanism as a treatment option, it is equally important to organize and understand amyloid disaggregation strategies. Disaggregation strategies are important and crucial as they are present innately functional in many living systems and dissolution of preformed amyloids may provide a direct benefit in many pathological conditions. In this review, we have compiled the known amyloid disaggregation mechanism, interactions, and possibilities of using disaggregases as a treatment option for amyloidosis. Methods We have provided the structural details using protein-ligand docking models to visualize the interaction between these disaggregases with amyloid fibrils and their respective proposed amyloid disaggregation mechanisms. Results After reviewing and comparing the different amyloid disaggregase systems and their proposed mechanisms, we presented two different hypotheses for ATP independent disaggregases using L-PGDS as a model. Conclusion Finally, we have highlighted the importance of understanding the underlying disaggregation mechanisms used by these chaperones and organic compounds before the implementation of these disaggregases as a potential treatment option for amyloidosis.
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21
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Ryabova N, Fakhranurova L, Balobanov V, Marchenkov V, Glukhov A, Ilyina N, Kochetov A, Suvorina M, Surin A, Katina N. Carbonic anhydrase amyloid fibrils composed of laterally associated protofilaments show reduced cytotoxicity. Biochem Biophys Res Commun 2022; 593:46-51. [DOI: 10.1016/j.bbrc.2022.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 11/26/2022]
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22
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Matsuo T, De Francesco A, Peters J. Molecular Dynamics of Lysozyme Amyloid Polymorphs Studied by Incoherent Neutron Scattering. Front Mol Biosci 2022; 8:812096. [PMID: 35111814 PMCID: PMC8801425 DOI: 10.3389/fmolb.2021.812096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.
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Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Japan
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
| | - Alessio De Francesco
- Institut Laue-Langevin, Grenoble, France
- CNR-IOM and INSIDE@ILL C/O Operative Group in Grenoble (OGG), Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institut Universitaire de France, Paris, France
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
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23
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Anselmo S, Sancataldo G, Mørck Nielsen H, Foderà V, Vetri V. Peptide-Membrane Interactions Monitored by Fluorescence Lifetime Imaging: A Study Case of Transportan 10. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13148-13159. [PMID: 34714654 PMCID: PMC8582253 DOI: 10.1021/acs.langmuir.1c02392] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The interest on detailed analysis of peptide-membrane interactions is of great interest in both fundamental and applied sciences as these may relate to both functional and pathogenic events. Such interactions are highly dynamic and spatially heterogeneous, making the investigation of the associated phenomena highly complex. The specific properties of membranes and peptide structural details, together with environmental conditions, may determine different events at the membrane interface, which will drive the fate of the peptide-membrane system. Here, we use an experimental approach based on the combination of spectroscopy and fluorescence microscopy methods to characterize the interactions of the multifunctional amphiphilic peptide transportan 10 with model membranes. Our approach, based on the use of suitable fluorescence reporters, exploits the advantages of phasor plot analysis of fluorescence lifetime imaging microscopy measurements to highlight the molecular details of occurring membrane alterations in terms of rigidity and hydration. Simultaneously, it allows following dynamic events in real time without sample manipulation distinguishing, with high spatial resolution, whether the peptide is adsorbed to or inserted in the membrane.
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Affiliation(s)
- Sara Anselmo
- Dipartimento
di Fisica e Chimica−Emilio Segré, Università degli Studi di Palermo, Viale delle Scienze ed. 18 90128, Palermo, Italy
| | - Giuseppe Sancataldo
- Dipartimento
di Fisica e Chimica−Emilio Segré, Università degli Studi di Palermo, Viale delle Scienze ed. 18 90128, Palermo, Italy
| | - Hanne Mørck Nielsen
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2 2100, Copenhagen, Denmark
| | - Vito Foderà
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2 2100, Copenhagen, Denmark
| | - Valeria Vetri
- Dipartimento
di Fisica e Chimica−Emilio Segré, Università degli Studi di Palermo, Viale delle Scienze ed. 18 90128, Palermo, Italy
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24
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Good SC, Dewison KM, Radford SE, van Oosten-Hawle P. Global Proteotoxicity Caused by Human β 2 Microglobulin Variants Impairs the Unfolded Protein Response in C. elegans. Int J Mol Sci 2021; 22:10752. [PMID: 34639093 PMCID: PMC8509642 DOI: 10.3390/ijms221910752] [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: 07/31/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Aggregation of β2 microglobulin (β2m) into amyloid fibrils is associated with systemic amyloidosis, caused by the deposition of amyloid fibrils containing the wild-type protein and its truncated variant, ΔN6 β2m, in haemo-dialysed patients. A second form of familial systemic amyloidosis caused by the β2m variant, D76N, results in amyloid deposits in the viscera, without renal dysfunction. Although the folding and misfolding mechanisms of β2 microglobulin have been widely studied in vitro and in vivo, we lack a comparable understanding of the molecular mechanisms underlying toxicity in a cellular and organismal environment. Here, we established transgenic C. elegans lines expressing wild-type (WT) human β2m, or the two highly amyloidogenic naturally occurring variants, D76N β2m and ΔN6 β2m, in the C. elegans bodywall muscle. Nematodes expressing the D76N β2m and ΔN6 β2m variants exhibit increased age-dependent and cell nonautonomous proteotoxicity associated with reduced motility, delayed development and shortened lifespan. Both β2m variants cause widespread endogenous protein aggregation contributing to the increased toxicity in aged animals. We show that expression of β2m reduces the capacity of C. elegans to cope with heat and endoplasmic reticulum (ER) stress, correlating with a deficiency to upregulate BiP/hsp-4 transcripts in response to ER stress in young adult animals. Interestingly, protein secretion in all β2m variants is reduced, despite the presence of the natural signal sequence, suggesting a possible link between organismal β2m toxicity and a disrupted ER secretory metabolism.
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Affiliation(s)
| | | | | | - Patricija van Oosten-Hawle
- Faculty of Biological Sciences, School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (S.C.G.); (K.M.D.); (S.E.R.)
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25
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Amyloid particles facilitate surface-catalyzed cross-seeding by acting as promiscuous nanoparticles. Proc Natl Acad Sci U S A 2021; 118:2104148118. [PMID: 34462352 PMCID: PMC8433567 DOI: 10.1073/pnas.2104148118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Amyloid seeds are nanometer-sized protein particles that accelerate amyloid assembly as well as propagate and transmit the amyloid protein conformation associated with a wide range of protein misfolding diseases. However, seeded amyloid growth through templated elongation at fibril ends cannot explain the full range of molecular behaviors observed during cross-seeded formation of amyloid by heterologous seeds. Here, we demonstrate that amyloid seeds can accelerate amyloid formation via a surface catalysis mechanism without propagating the specific amyloid conformation associated with the seeds. This type of seeding mechanism is demonstrated through quantitative characterization of the cross-seeded assembly reactions involving two nonhomologous and unrelated proteins: the human Aβ42 peptide and the yeast prion-forming protein Sup35NM. Our results demonstrate experimental approaches to differentiate seeding by templated elongation from nontemplated amyloid seeding and rationalize the molecular mechanism of the cross-seeding phenomenon as a manifestation of the aberrant surface activities presented by amyloid seeds as nanoparticles.
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26
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Identification of transmissible proteotoxic oligomer-like fibrils that expand conformational diversity of amyloid assemblies. Commun Biol 2021; 4:939. [PMID: 34354242 PMCID: PMC8342456 DOI: 10.1038/s42003-021-02466-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
Protein misfolding and amyloid deposition are associated with numerous diseases. The detailed characterization of the proteospecies mediating cell death remains elusive owing to the (supra)structural polymorphism and transient nature of the assemblies populating the amyloid pathway. Here we describe the identification of toxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). While N21Q filaments share structural properties with cytocompatible fibrils, including the 4.7 Å inter-strand distance and β-sheet-rich conformation, they concurrently display characteristics of oligomers, such as low thioflavin-T binding, high surface hydrophobicity and recognition by the A11 antibody, leading to high potency to disrupt membranes and cause cellular dysfunction. The toxic oligomer-like conformation of N21Q fibrils, which is preserved upon elongation, is transmissible to naïve IAPP. These stable fibrils expanding the conformational diversity of amyloid assemblies represent an opportunity to elucidate the structural basis of amyloid disorders. Nguyen et al identified cytotoxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). They presented evidence to show that these stable fibrils expand the conformational diversity of amyloid assemblies, which represents an opportunity to elucidate the structural basis of amyloid disorders.
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27
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Morris C, Kent TW, Shen F, Wojcikiewicz EP, Du D. Effects of the Hydrophilic N-Terminal Region on Aβ-Mediated Membrane Disruption. J Phys Chem B 2021; 125:7671-7678. [PMID: 34252282 DOI: 10.1021/acs.jpcb.1c03413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Amyloidogenesis of amyloid-β (Aβ) peptides is intimately related to pathological neurodegeneration in Alzheimer's disease. Here, we investigated the membrane damage activity of Aβ40 and its derivatives that contain mutation at the N-terminal charged residues using a membrane leakage assay. A model 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) phospholipid vesicle encapsulating the fluorescent dye carboxyfluorescein was used in the study. Our results show that the mutations of the N-terminal charged residues of Aβ40 significantly affect the peptide-induced membrane leakage. The results suggest that favorable electrostatic interactions of the N-terminal charged residues and the phosphatidylcholine membrane surface are crucial in Aβ-mediated membrane permeation. The flexible and charge-rich N-terminal region may play a critical role in directing Aβ self-association on the membrane surface and in anchoring and stabilizing the peptide aggregates inserted in the phospholipid membrane, which are closely related with membrane disruption activity of Aβ. The results provide new mechanistic insight into the Aβ-mediated membrane damage process, which may be critical for understanding the mechanism of Aβ neurotoxicity in Alzheimer's disease.
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Affiliation(s)
- Clifford Morris
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Thomas W Kent
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Fengyun Shen
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Ewa P Wojcikiewicz
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Deguo Du
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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28
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Lutter L, Aubrey LD, Xue WF. On the Structural Diversity and Individuality of Polymorphic Amyloid Protein Assemblies. J Mol Biol 2021; 433:167124. [PMID: 34224749 DOI: 10.1016/j.jmb.2021.167124] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/20/2021] [Accepted: 06/26/2021] [Indexed: 12/24/2022]
Abstract
The prediction of highly ordered three-dimensional structures of amyloid protein fibrils from the amino acid sequences of their monomeric self-assembly precursors constitutes a challenging and unresolved aspect of the classical protein folding problem. Because of the polymorphic nature of amyloid assembly whereby polypeptide chains of identical amino acid sequences under identical conditions are capable of self-assembly into a spectrum of different fibril structures, the prediction of amyloid structures from an amino acid sequence requires a detailed and holistic understanding of its assembly free energy landscape. The full extent of the structure space accessible to the cross-β molecular architecture of amyloid must also be resolved. Here, we review the current understanding of the diversity and the individuality of amyloid structures, and how the polymorphic landscape of amyloid links to biology and disease phenotypes. We present a comprehensive review of structural models of amyloid fibrils derived by cryo-EM, ssNMR and AFM to date, and discuss the challenges ahead for resolving the structural basis and the biological consequences of polymorphic amyloid assemblies.
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Affiliation(s)
- Liisa Lutter
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Liam D Aubrey
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Wei-Feng Xue
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK.
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29
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Brown A, Török M. Functional amyloids in the human body. Bioorg Med Chem Lett 2021; 40:127914. [PMID: 33691165 DOI: 10.1016/j.bmcl.2021.127914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 11/18/2022]
Abstract
Amyloids have long been associated with a variety of human degenerative diseases. Discoveries indicate, however, that there are several amyloids that serve functional roles in the human body. These amyloids are involved in a variety of biological processes ranging from storage of peptide hormones to necroptosis of cells. Additionally, there are distinct differences between toxic amyloids and their functional counterparts including kinetics of assembly/disassembly and structural features. This digest article surveys the biological roles of functional amyloids found in the human body, key differences between functional and toxic amyloids, and potential therapeutic applications.
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Affiliation(s)
- Amy Brown
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Marianna Török
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA.
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30
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Ilyinsky NS, Nesterov SV, Shestoperova EI, Fonin AV, Uversky VN, Gordeliy VI. On the Role of Normal Aging Processes in the Onset and Pathogenesis of Diseases Associated with the Abnormal Accumulation of Protein Aggregates. BIOCHEMISTRY (MOSCOW) 2021; 86:275-289. [PMID: 33838629 DOI: 10.1134/s0006297921030056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aging is a prime systemic cause of various age-related diseases, in particular, proteinopathies. In fact, most diseases associated with protein misfolding are sporadic, and their incidence increases with aging. This review examines the process of protein aggregate formation, the toxicity of such aggregates, the organization of cellular systems involved in proteostasis, and the impact of protein aggregates on important cellular processes leading to proteinopathies. We also analyze how manifestations of aging (mitochondrial dysfunction, dysfunction of signaling systems, changes in the genome and epigenome) facilitate pathogenesis of various proteinopathies either directly, by increasing the propensity of key proteins for aggregation, or indirectly, through dysregulation of stress responses. Such analysis might help in outlining approaches for treating proteinopathies and extending healthy longevity.
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Affiliation(s)
- Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institute of Cytochemistry and Molecular Pharmacology, Moscow, 115404, Russia
| | - Elizaveta I Shestoperova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexander V Fonin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Forschungszentrum Juelich, Juelich, 52428, Germany.,Institut de Biologie Structurale, Grenoble, 38000, France
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31
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Kong KYE, Coelho JPL, Feige MJ, Khmelinskii A. Quality control of mislocalized and orphan proteins. Exp Cell Res 2021; 403:112617. [PMID: 33930402 DOI: 10.1016/j.yexcr.2021.112617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022]
Abstract
A healthy and functional proteome is essential to cell physiology. However, this is constantly being challenged as most steps of protein metabolism are error-prone and changes in the physico-chemical environment can affect protein structure and function, thereby disrupting proteome homeostasis. Among a variety of potential mistakes, proteins can be targeted to incorrect compartments or subunits of protein complexes may fail to assemble properly with their partners, resulting in the formation of mislocalized and orphan proteins, respectively. Quality control systems are in place to handle these aberrant proteins, and to minimize their detrimental impact on cellular functions. Here, we discuss recent findings on quality control mechanisms handling mislocalized and orphan proteins. We highlight common principles involved in their recognition and summarize how accumulation of these aberrant molecules is associated with aging and disease.
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Affiliation(s)
| | - João P L Coelho
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Matthias J Feige
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
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32
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Abstract
The molecular architecture of α-Synuclein (α-Syn) inclusions, pathognomonic of various neurodegenerative disorders, remains unclear. α-Syn inclusions were long thought to consist mainly of α-Syn fibrils, but recent reports pointed to intracellular membranes as the major inclusion component. Here, we use cryo-electron tomography (cryo-ET) to image neuronal α-Syn inclusions in situ at molecular resolution. We show that inclusions seeded by α-Syn aggregates produced recombinantly or purified from patient brain consist of α-Syn fibrils crisscrossing a variety of cellular organelles. Using gold-labeled seeds, we find that aggregate seeding is predominantly mediated by small α-Syn fibrils, from which cytoplasmic fibrils grow unidirectionally. Detailed analysis of membrane interactions revealed that α-Syn fibrils do not contact membranes directly, and that α-Syn does not drive membrane clustering. Altogether, we conclusively demonstrate that neuronal α-Syn inclusions consist of α-Syn fibrils intermixed with membranous organelles, and illuminate the mechanism of aggregate seeding and cellular interaction.
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33
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Identification of critical amino acid residues in the regulatory N-terminal domain of PMEL. Sci Rep 2021; 11:7730. [PMID: 33833328 PMCID: PMC8032716 DOI: 10.1038/s41598-021-87259-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/26/2021] [Indexed: 01/22/2023] Open
Abstract
The pigment cell-specific protein PMEL forms a functional amyloid matrix in melanosomes onto which the pigment melanin is deposited. The amyloid core consists of a short proteolytic fragment, which we have termed the core-amyloid fragment (CAF) and perhaps additional parts of the protein, such as the PKD domain. A highly O-glycosylated repeat (RPT) domain also derived from PMEL proteolysis associates with the amyloid and is necessary to establish the sheet-like morphology of the assemblies. Excluded from the aggregate is the regulatory N-terminus, which nevertheless must be linked in cis to the CAF in order to drive amyloid formation. The domain is then likely cleaved away immediately before, during, or immediately after the incorporation of a new CAF subunit into the nascent amyloid. We had previously identified a 21 amino acid long region, which mediates the regulatory activity of the N-terminus towards the CAF. However, many mutations in the respective segment caused misfolding and/or blocked PMEL export from the endoplasmic reticulum, leaving their phenotype hard to interpret. Here, we employ a saturating mutagenesis approach targeting the motif at single amino acid resolution. Our results confirm the critical nature of the PMEL N-terminal region and identify several residues essential for PMEL amyloidogenesis.
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34
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Tian Y, Liang R, Kumar A, Szwedziak P, Viles JH. 3D-visualization of amyloid-β oligomer interactions with lipid membranes by cryo-electron tomography. Chem Sci 2021; 12:6896-6907. [PMID: 34123318 PMCID: PMC8153238 DOI: 10.1039/d0sc06426b] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Amyloid-β (Aβ) assemblies have been shown to bind to lipid bilayers. This can disrupt membrane integrity and cause a loss of cellular homeostasis, that triggers a cascade of events leading to Alzheimer's disease. However, molecular mechanisms of Aβ cytotoxicity and how the different assembly forms interact with the membrane remain enigmatic. Here we use cryo-electron tomography (cryoET) to obtain three-dimensional nano-scale images of various Aβ assembly types and their interaction with liposomes. Aβ oligomers and curvilinear protofibrils bind extensively to the lipid vesicles, inserting and carpeting the upper-leaflet of the bilayer. Aβ oligomers concentrate at the interface of vesicles and form a network of Aβ-linked liposomes, while crucially, monomeric and fibrillar Aβ have relatively little impact on the membrane. Changes to lipid membrane composition highlight a significant role for GM1-ganglioside in promoting Aβ-membrane interactions. The different effects of Aβ assembly forms observed align with the highlighted cytotoxicity reported for Aβ oligomers. The wide-scale incorporation of Aβ oligomers and curvilinear protofibrils into the lipid bilayer suggests a mechanism by which membrane integrity is lost. Cryo-electron tomography 3D imaging of amyloid-β oligomers carpeting the surface of lipid bilayers in near native conditions.![]()
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Affiliation(s)
- Yao Tian
- School of Biological and Chemical Sciences, Queen Mary University of London Mile End Road London E1 4NS UK
| | - Ruina Liang
- School of Biological and Chemical Sciences, Queen Mary University of London Mile End Road London E1 4NS UK
| | - Amit Kumar
- School of Biological and Chemical Sciences, Queen Mary University of London Mile End Road London E1 4NS UK
| | - Piotr Szwedziak
- Laboratory of Structural Cell Biology, Centre of New Technologies, University of Warsaw 02-097 Warsaw Poland .,ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw 02-097 Warsaw Poland
| | - John H Viles
- School of Biological and Chemical Sciences, Queen Mary University of London Mile End Road London E1 4NS UK
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35
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Deo T, Cheng Q, Paul S, Qiang W, Potapov A. Application of DNP-enhanced solid-state NMR to studies of amyloid-β peptide interaction with lipid membranes. Chem Phys Lipids 2021; 236:105071. [PMID: 33716023 DOI: 10.1016/j.chemphyslip.2021.105071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/13/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022]
Abstract
The cellular membrane disruption induced by the aggregation of Aβ peptide has been proposed as a plausible cause of neuronal cell death during Alzheimer's disease. The molecular-level details of the Aβ interaction with cellular membranes were previously probed using solid state NMR (ssNMR), however, due to the limited sensitivity of the latter, studies were limited to samples with high Aβ-to-lipid ratio. The dynamic nuclear polarization (DNP) is a technique for increasing the sensitivity of NMR. In this work we demonstrate the feasibility of DNP-enhanced ssNMR studies of Aβ40 peptide interacting with various model liposomes: (1) a mixture of zwitterionic 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) and negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG); (2) a mixture of POPC, POPG, cholesterol, sphingomyelin and ganglioside GM1; (3) the synaptic plasma membrane vesicles (SPMVs) extracted from rat brain tissues. In addition, DNP-ssNMR was applied to capturing changes in Aβ40 conformation taking place upon the peptide insertion into POPG liposomes. The signal enhancements under conditions of DNP allow carrying out informative 2D ssNMR experiments with about 0.25 mg of Aβ40 peptides (i.e. reaching Aβ40-to-lipid ratio of 1:200). In the studied liposome models, the 13C NMR chemical shifts at many 13C-labelled sites of Aβ40 are characteristic of β-sheets. In addition, in POPG liposomes the peptide forms hydrophobic contacts F19-L34 and F19-I32. Both the chemical shifts and hydrophobic contacts of Aβ40 in POPG remain the same before and after 8 h of incubation. This suggests that conformation at the 13C-labelled sites of the peptide is similar before and after the insertion process. Overall, our results demonstrate that DNP helps to overcome the sensitivity limitation of ssNMR, and thereby expand the applicability of ssNMR for charactering the Aβ peptide interacting with lipids.
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Affiliation(s)
- Thomas Deo
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Qinghui Cheng
- Department of Chemistry, Binghamton University, the State University of New York, Binghamton, NY, 13902, USA
| | - Subhadip Paul
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Wei Qiang
- Department of Chemistry, Binghamton University, the State University of New York, Binghamton, NY, 13902, USA
| | - Alexey Potapov
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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36
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Stockmann J, Verberk IMW, Timmesfeld N, Denz R, Budde B, Lange-Leifhelm J, Scheltens P, van der Flier WM, Nabers A, Teunissen CE, Gerwert K. Amyloid-β misfolding as a plasma biomarker indicates risk for future clinical Alzheimer's disease in individuals with subjective cognitive decline. ALZHEIMERS RESEARCH & THERAPY 2020; 12:169. [PMID: 33357241 PMCID: PMC7761044 DOI: 10.1186/s13195-020-00738-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022]
Abstract
Background We evaluated Aβ misfolding in combination with Aβ42/40 ratio as a prognostic tool for future clinical progression to mild cognitive impairment (MCI) or dementia due to Alzheimer’s disease (AD) in individuals with subjective cognitive decline (SCD). Methods Baseline plasma samples (n = 203) from SCD subjects in the SCIENCe project and Amsterdam Dementia Cohort (age 61 ± 9 years; 57% male, mean follow-up time 2.7 years) were analyzed using immuno-infrared-sensor technology. Within 6 years of follow-up, 22 (11%) individuals progressed to MCI or dementia due to AD. Sensor readout values > 1646 cm− 1 reflected normal Aβ folding; readouts at ≤ 1646 cm− 1 reflected low and at < 1644 cm− 1 high misfolding. We used Cox proportional hazard models to quantify Aβ misfolding as a prognostic biomarker for progression to MCI and dementia due to AD. The accuracy of the predicted development of MCI/AD was determined by time-dependent receiver operating characteristic (t-ROC) curve analyses that take individual follow-up and conversion times into account. Statistical models were adjusted for age, sex, and APOEε4 status. Additionally, plasma Aβ42/40 data measured by SIMOA were statistically analyzed and compared. Results All 22 patients who converted to MCI or AD-dementia within 6 years exhibited Aβ misfolding at baseline. Cox analyses revealed a hazard ratio (HR) of 19 (95% confidence interval [CI] 2.2–157.8) for future conversion of SCD subjects with high misfolding and of 11 (95% CI 1.0–110.1) for those with low misfolding. T-ROC curve analyses yielded an area under the curve (AUC) of 0.94 (95% CI 0.86–1.00; 6-year follow-up) for Aβ misfolding in an age, sex, and APOEε4 model. A similar model with plasma Aβ42/40 ratio yielded an AUC of 0.92 (95% CI, 0.82–1.00). The AUC increased to 0.99 (95% CI, 0.99–1.00) after inclusion of both Aβ misfolding and the Aβ42/40 ratio. Conclusions A panel of structure- and concentration-based plasma amyloid biomarkers may predict conversion to clinical MCI and dementia due to AD in cognitively unimpaired subjects. These plasma biomarkers provide a noninvasive and cost-effective alternative for screening early AD pathological changes. Follow-up studies and external validation in larger cohorts are in progress for further validation of our findings. Supplementary Information The online version contains supplementary material available at 10.1186/s13195-020-00738-8.
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Affiliation(s)
- Julia Stockmann
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.,Department of Biophysics, Ruhr University Bochum, Faculty of Biology and Biotechnology, Bochum, Germany
| | - Inge M W Verberk
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Nina Timmesfeld
- Ruhr University Bochum, Department of Medical Informatics, Biometry and Epidemiology, Bochum, Germany
| | - Robin Denz
- Ruhr University Bochum, Department of Medical Informatics, Biometry and Epidemiology, Bochum, Germany
| | - Brian Budde
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.,Department of Biophysics, Ruhr University Bochum, Faculty of Biology and Biotechnology, Bochum, Germany
| | - Julia Lange-Leifhelm
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.,Department of Biophysics, Ruhr University Bochum, Faculty of Biology and Biotechnology, Bochum, Germany
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Andreas Nabers
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany.,Department of Biophysics, Ruhr University Bochum, Faculty of Biology and Biotechnology, Bochum, Germany
| | - Charlotte E Teunissen
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Klaus Gerwert
- Competence Center for Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr-University Bochum, Bochum, Germany. .,Department of Biophysics, Ruhr University Bochum, Faculty of Biology and Biotechnology, Bochum, Germany.
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37
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Pallbo J, Imai M, Gentile L, Takata SI, Olsson U, Sparr E. NACore Amyloid Formation in the Presence of Phospholipids. Front Physiol 2020; 11:592117. [PMID: 33391013 PMCID: PMC7775532 DOI: 10.3389/fphys.2020.592117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/02/2020] [Indexed: 11/20/2022] Open
Abstract
Amyloids are implicated in many diseases, and disruption of lipid membrane structures is considered as one possible mechanism of pathology. In this paper we investigate interactions between an aggregating peptide and phospholipid membranes, focusing on the nanometer-scale structures of the aggregates formed, as well as on the effect on the aggregation process. As a model system, we use the small amyloid-forming peptide named NACore, which is a fragment of the central region of the protein α-synuclein that is associated with Parkinson's disease. We find that phospholipid vesicles readily associate with the amyloid fibril network in the form of highly distorted and trapped vesicles that also may wet the surface of the fibrils. This effect is most pronounced for model lipid systems containing only zwitterionic lipids. Fibrillation is found to be retarded by the presence of the vesicles. At the resolution of our measurements, which are based mainly on cryogenic transmission electron microscopy (cryo-TEM), X-ray scattering, and circular dichroism (CD) spectroscopy, we find that the resulting aggregates can be well fitted as linear combinations of peptide fibrils and phospholipid bilayers. There are no detectable effects on the cross-β packing of the peptide molecules in the fibrils, or on the thickness of the phospholipid bilayers. This suggests that while the peptide fibrils and lipid bilayers readily co-assemble on large length-scales, most of them still retain their separate structural identities on molecular length-scales. Comparison between this relatively simple model system and other amyloid systems might help distinguish aspects of amyloid-lipid interactions that are generic from aspects that are more protein specific. Finally, we briefly consider possible implications of the obtained results for in-vivo amyloid toxicity.
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Affiliation(s)
- Jon Pallbo
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Luigi Gentile
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
| | | | - Ulf Olsson
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Department of Chemistry, Lund University, Lund, Sweden
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38
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Jaiswal N, Agarwal N, Poluri KM, Kumar D. Effect of urea concentration on instant refolding of Nuclear Export Protein (NEP) from Influenza-A virus H1N1: A solution NMR based investigation. Int J Biol Macromol 2020; 165:2508-2519. [PMID: 33470198 DOI: 10.1016/j.ijbiomac.2020.10.146] [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: 08/26/2019] [Revised: 08/12/2020] [Accepted: 10/18/2020] [Indexed: 01/14/2023]
Abstract
Nuclear-export-protein (NEP) plays multiple-functions during influenza virus replication-cycle and shows unique pattern of conserved residues, which altogether make NEP a potential target for developing novel anti-influenza drugs. However, the mechanistic structural biology of NEP has not been fully characterized so far owing to its tendency to aggregate in solution. As structural information is important to guide rational drug-discovery process; therefore, procedural optimization efforts are going on to achieve properly folded NEP in sub-millimolar concentrations for solution-NMR investigations. As a first step in this direction, the refolding-cum-aggregation behavior of recombinant-NEP with N-terminal purification-tag (referred here as NEPN) at different urea-concentrations has been investigated here by NMR-based methods. Several attempts were made to refold denatured NEP-N through step-dialysis. However, owing to its strong tendency to aggregate, excessive precipitation was observed at sub-higher levels of urea concentration (5.0 ± 1.0 M). Finally, we used drip-dilution method with 10.5 M urea-denatured NEP-N and were able to refold NEP-N instantly. The amide 1H dispersion of 3.6 ppm (6.6-10.2 ppm) in the 15N-HSQC-spectra of instantly refolded NEP-N confirmed the folded state. This successful instant-refolding of NEP-N has been reported for the first-time and the underlying mechanism has been rationalized through establishing the complete backbone-resonance-assignments of NEP-N at 9.7 M urea-denatured state.
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Affiliation(s)
- Nancy Jaiswal
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, India; Dr. APJ Abdul Kalam Technical University, IET Campus, Sitapur Road, Lucknow, Uttar Pradesh, India
| | - Nipanshu Agarwal
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, India.
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Ulamec SM, Brockwell DJ, Radford SE. Looking Beyond the Core: The Role of Flanking Regions in the Aggregation of Amyloidogenic Peptides and Proteins. Front Neurosci 2020; 14:611285. [PMID: 33335475 PMCID: PMC7736610 DOI: 10.3389/fnins.2020.611285] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Amyloid proteins are involved in many neurodegenerative disorders such as Alzheimer’s disease [Tau, Amyloid β (Aβ)], Parkinson’s disease [alpha-synuclein (αSyn)], and amyotrophic lateral sclerosis (TDP-43). Driven by the early observation of the presence of ordered structure within amyloid fibrils and the potential to develop inhibitors of their formation, a major goal of the amyloid field has been to elucidate the structure of the amyloid fold at atomic resolution. This has now been achieved for a wide variety of sequences using solid-state NMR, microcrystallography, X-ray fiber diffraction and cryo-electron microscopy. These studies, together with in silico methods able to predict aggregation-prone regions (APRs) in protein sequences, have provided a wealth of information about the ordered fibril cores that comprise the amyloid fold. Structural and kinetic analyses have also shown that amyloidogenic proteins often contain less well-ordered sequences outside of the amyloid core (termed here as flanking regions) that modulate function, toxicity and/or aggregation rates. These flanking regions, which often form a dynamically disordered “fuzzy coat” around the fibril core, have been shown to play key parts in the physiological roles of functional amyloids, including the binding of RNA and in phase separation. They are also the mediators of chaperone binding and membrane binding/disruption in toxic amyloid assemblies. Here, we review the role of flanking regions in different proteins spanning both functional amyloid and amyloid in disease, in the context of their role in aggregation, toxicity and cellular (dys)function. Understanding the properties of these regions could provide new opportunities to target disease-related aggregation without disturbing critical biological functions.
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Affiliation(s)
- Sabine M Ulamec
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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40
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Quercetin Disaggregates Prion Fibrils and Decreases Fibril-Induced Cytotoxicity and Oxidative Stress. Pharmaceutics 2020; 12:pharmaceutics12111081. [PMID: 33187342 PMCID: PMC7696844 DOI: 10.3390/pharmaceutics12111081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/17/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative diseases caused by misfolding and aggregation of prion protein (PrP). Previous studies have demonstrated that quercetin can disaggregate some amyloid fibrils, such as amyloid β peptide (Aβ) and α-synuclein. However, the disaggregating ability is unclear in PrP fibrils. In this study, we examined the amyloid fibril-disaggregating activity of quercetin on mouse prion protein (moPrP) and characterized quercetin-bound moPrP fibrils by imaging, proteinase resistance, hemolysis assay, cell viability, and cellular oxidative stress measurements. The results showed that quercetin treatment can disaggregate moPrP fibrils and lead to the formation of the proteinase-sensitive amorphous aggregates. Furthermore, quercetin-bound fibrils can reduce the membrane disruption of erythrocytes. Consequently, quercetin-bound fibrils cause less oxidative stress, and are less cytotoxic to neuroblastoma cells. The role of quercetin is distinct from the typical function of antiamyloidogenic drugs that inhibit the formation of amyloid fibrils. This study provides a solution for the development of antiamyloidogenic therapy.
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Beal DM, Tournus M, Marchante R, Purton TJ, Smith DP, Tuite MF, Doumic M, Xue WF. The Division of Amyloid Fibrils: Systematic Comparison of Fibril Fragmentation Stability by Linking Theory with Experiments. iScience 2020; 23:101512. [PMID: 32920487 PMCID: PMC7492994 DOI: 10.1016/j.isci.2020.101512] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/31/2020] [Accepted: 08/26/2020] [Indexed: 01/22/2023] Open
Abstract
The division of amyloid protein fibrils is required for the propagation of the amyloid state and is an important contributor to their stability, pathogenicity, and normal function. Here, we combine kinetic nanoscale imaging experiments with analysis of a mathematical model to resolve and compare the division stability of amyloid fibrils. Our theoretical results show that the division of any type of filament results in self-similar length distributions distinct to each fibril type and the conditions applied. By applying these theoretical results to profile the dynamical stability toward breakage for four different amyloid types, we reveal particular differences in the division properties of disease-related amyloid formed from α-synuclein when compared with non-disease associated model amyloid, the former showing lowered intrinsic stability toward breakage and increased likelihood of shedding smaller particles. Our results enable the comparison of protein filaments' intrinsic dynamic stabilities, which are key to unraveling their toxic and infectious potentials.
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Affiliation(s)
- David M. Beal
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Magali Tournus
- Centrale Marseille, I2M, UMR 7373, CNRS, Aix-Marseille Univ., Marseille 13453, France
| | - Ricardo Marchante
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Tracey J. Purton
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - David P. Smith
- Biomolecular Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Mick F. Tuite
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Marie Doumic
- INRIA Rocquencourt, équipe-projet BANG, Domaine de Voluceau, BP 105, 78153 Rocquencourt, France
- Wolfgang Pauli Institute, University of Vienna, Vienna, Austria
| | - Wei-Feng Xue
- Kent Fungal Group, School of Biosciences, University of Kent, CT2 7NJ Canterbury, UK
- INRIA Rocquencourt, équipe-projet BANG, Domaine de Voluceau, BP 105, 78153 Rocquencourt, France
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Investigating the Structure of Neurotoxic Protein Aggregates Inside Cells. Trends Cell Biol 2020; 30:951-966. [PMID: 32981805 DOI: 10.1016/j.tcb.2020.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022]
Abstract
Neurodegenerative diseases affect the lives of millions of people across the world, being particularly prevalent in the aging population. Despite huge research efforts, conclusive insights into the disease mechanisms are still lacking. Therefore, therapeutic strategies are limited to symptomatic treatments. A common histopathological hallmark of many neurodegenerative diseases is the presence of large pathognomonic protein aggregates, but their role in the disease pathology is unclear and subject to controversy. Here, we discuss imaging methods allowing investigation of these structures within their cellular environment: conventional electron microscopy (EM), super-resolution light microscopy (SR-LM), and cryo-electron tomography (cryo-ET). Multidisciplinary approaches are key for understanding neurodegenerative diseases and may contribute to the development of effective treatments. For simplicity, we focus on huntingtin aggregates, characteristic of Huntington's disease.
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Feng Q, Hong Y, Pradeep Nidamanuri N, Yang C, Li Q, Dong M. Identification and Nanomechanical Characterization of the HIV Tat-Amyloid β Peptide Multifibrillar Structures. Chemistry 2020; 26:9449-9453. [PMID: 32167218 DOI: 10.1002/chem.201905715] [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: 12/18/2019] [Revised: 02/29/2020] [Indexed: 12/25/2022]
Abstract
HIV transactivator of transcription (Tat) protein could interact with amyloid β (Aβ) peptide which cause the growth of Aβ plaques in the brain and result in Alzheimer's disease in HIV-infected patients. Herein, we employ high-resolution atomic force microscopy and quantitative nanomechanical mapping to investigate the effects of Tat protein in Aβ peptide aggregation. Our results demonstrate that the Tat protein could bind to the Aβ fibril surfaces and result in the formation of Tat-Aβ multifibrillar structures. The resultant Tat-Aβ multifibrillar aggregates represent an increase in stiffness compared with Aβ fibrils due to the increase in β-sheet formation. The identification and characterization of the Tat-Aβ intermediate aggregates is important to understanding the interactions between Tat protein and Aβ peptide, and the development of novel therapeutic strategy for Alzheimer's disease-like disorder in HIV infected individuals.
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Affiliation(s)
- Qiying Feng
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Yue Hong
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Naga Pradeep Nidamanuri
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Chuanxu Yang
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Mingdong Dong
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of, Education, and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
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The Effect of (-)-Epigallocatechin-3-Gallate on the Amyloid-β Secondary Structure. Biophys J 2020; 119:349-359. [PMID: 32579965 DOI: 10.1016/j.bpj.2020.05.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/20/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023] Open
Abstract
Amyloid-β (Aβ) is a macromolecular structure of great interest because its misfolding and aggregation, along with changes in the secondary structure, have been correlated with its toxicity in various neurodegenerative diseases. Small drug-like molecules can modulate the amyloid secondary structure and therefore have raised significant interest in applications to active and passive therapies targeting amyloids. In this study, we investigate the interactions of epigallocatechin-3-gallate (EGCG), found in green tea, with Aβ polypeptides, using a combination of in vitro immuno-infrared sensor measurements, docking, molecular dynamics simulations, and ab initio calculations. We find that the interactions of EGCG are dominated by only a few residues in the fibrils, including hydrophobic π-π interactions with aromatic rings of side chains and hydrophilic interactions with the backbone of Aβ, as confirmed by extended (1-μs-long) molecular dynamics simulations. Immuno-infrared sensor data are consistent with degradation of Aβ fibril induced by EGCG and inhibition of Aβ fibril and oligomer formation, as manifested by the recovery of the amide-I band of monomeric Aβ, which is red-shifted by 26 cm-1 when compared to the amide-I band of the fibrillar form. The shift is rationalized by computations of the infrared spectra of Aβ42 model structures, suggesting that the conformational change involves interchain hydrogen bonds in the amyloid fibrils that are broken upon binding of EGCG.
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45
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Menon S, Sengupta N, Das P. Nanoscale Interplay of Membrane Composition and Amyloid Self-Assembly. J Phys Chem B 2020; 124:5837-5846. [DOI: 10.1021/acs.jpcb.0c03796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sneha Menon
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, India
| | - Payel Das
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Applied Physics and Applied Math Department, Columbia University, New York, New York 10027, United States
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46
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Dias CL, Jalali S, Yang Y, Cruz L. Role of Cholesterol on Binding of Amyloid Fibrils to Lipid Bilayers. J Phys Chem B 2020; 124:3036-3042. [DOI: 10.1021/acs.jpcb.0c00485] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Luis Cruz
- Department of Physics, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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47
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L. Almeida Z, M. M. Brito R. Structure and Aggregation Mechanisms in Amyloids. Molecules 2020; 25:molecules25051195. [PMID: 32155822 PMCID: PMC7179426 DOI: 10.3390/molecules25051195] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022] Open
Abstract
The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.
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48
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Abstract
Ageing is a major risk factor for the development of many diseases, prominently including neurodegenerative disorders such as Alzheimer disease and Parkinson disease. A hallmark of many age-related diseases is the dysfunction in protein homeostasis (proteostasis), leading to the accumulation of protein aggregates. In healthy cells, a complex proteostasis network, comprising molecular chaperones and proteolytic machineries and their regulators, operates to ensure the maintenance of proteostasis. These factors coordinate protein synthesis with polypeptide folding, the conservation of protein conformation and protein degradation. However, sustaining proteome balance is a challenging task in the face of various external and endogenous stresses that accumulate during ageing. These stresses lead to the decline of proteostasis network capacity and proteome integrity. The resulting accumulation of misfolded and aggregated proteins affects, in particular, postmitotic cell types such as neurons, manifesting in disease. Recent analyses of proteome-wide changes that occur during ageing inform strategies to improve proteostasis. The possibilities of pharmacological augmentation of the capacity of proteostasis networks hold great promise for delaying the onset of age-related pathologies associated with proteome deterioration and for extending healthspan.
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50
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Rudzińska M, Parodi A, Balakireva AV, Chepikova OE, Venanzi FM, Zamyatnin AA. Cellular Aging Characteristics and Their Association with Age-Related Disorders. Antioxidants (Basel) 2020; 9:antiox9020094. [PMID: 31979201 PMCID: PMC7071036 DOI: 10.3390/antiox9020094] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/12/2020] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Different molecular signaling pathways, biological processes, and intercellular communication mechanisms control longevity and are affected during cellular senescence. Recent data have suggested that organelle communication, as well as genomic and metabolic dysfunctions, contribute to this phenomenon. Oxidative stress plays a critical role by inducing structural modifications to biological molecules while affecting their function and catabolism and eventually contributing to the onset of age-related dysfunctions. In this scenario, proteins are not adequately degraded and accumulate in the cell cytoplasm as toxic aggregates, increasing cell senescence progression. In particular, carbonylation, defined as a chemical reaction that covalently and irreversibly modifies proteins with carbonyl groups, is considered to be a significant indicator of protein oxidative stress and aging. Here, we emphasize the role and dysregulation of the molecular pathways controlling cell metabolism and proteostasis, the complexity of the mechanisms that occur during aging, and their association with various age-related disorders. The last segment of the review details current knowledge on protein carbonylation as a biomarker of cellular senescence in the development of diagnostics and therapeutics for age-related dysfunctions.
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Affiliation(s)
- Magdalena Rudzińska
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.); (A.P.); (A.V.B.); (O.E.C.); (F.M.V.)
| | - Alessandro Parodi
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.); (A.P.); (A.V.B.); (O.E.C.); (F.M.V.)
| | - Anastasia V. Balakireva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.); (A.P.); (A.V.B.); (O.E.C.); (F.M.V.)
| | - Olga E. Chepikova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.); (A.P.); (A.V.B.); (O.E.C.); (F.M.V.)
| | - Franco M. Venanzi
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.); (A.P.); (A.V.B.); (O.E.C.); (F.M.V.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (M.R.); (A.P.); (A.V.B.); (O.E.C.); (F.M.V.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: ; Tel.: +74956229843
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