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Heravi S, Power JVD, Yethiraj A, Booth V. The effects of biological crowders on fibrillization, structure, diffusion, and conformational dynamics of α-synuclein. Protein Sci 2024; 33:e4894. [PMID: 38358134 PMCID: PMC10868423 DOI: 10.1002/pro.4894] [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: 09/15/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 02/16/2024]
Abstract
α-synuclein is an intrinsically disordered protein (IDP) whose aggregation in presynaptic neuronal cells is a pathological hallmark of Lewy body formation and Parkinson's disease. This aggregation process is likely affected by the crowded macromolecular cellular environment. In this study, α-synuclein was studied in the presence of both a synthetic crowder, Ficoll70, and a biological crowder composed of lysed cells that better mimics the biocomplexity of the cellular environment. 15 N-1 H HSQC NMR results show similar α-synuclein chemical shifts in non-crowded and all crowded conditions implying that it remains similarly unstructured in all conditions. Nevertheless, both HSQC NMR and fluorescence measurements indicate that, only in the cell lysate, α-synuclein forms aggregates over a timescale of 48 h. 15 N-edited diffusion measurements indicate that all crowders slow down the α-synuclein's diffusivity. Interestingly, at high concentrations, α-synuclein diffuses faster in cell lysate than in Ficoll70, possibly due to additional soft (e.g., electrostatic or hydrophobic) interactions. 15 N-edited relaxation measurements show that some residues are more mobile in cell lysate than in Ficoll70; the rates that are most different are predominantly in hydrophobic residues. We thus examined cell lysates with reduced hydrophobicity and found slower dynamics (higher relaxation rates) in several α-synuclein residues. Taken together, these experiments suggest that while cell lysate does not substantially affect α-synuclein structure (HSQC spectra), it does affect chain dynamics and translational diffusion, and strongly affects aggregation over a timescale of days, in a manner that is different from either no crowder or an artificial crowder: soft hydrophobic interactions are implicated.
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Affiliation(s)
- Sina Heravi
- Department of BiochemistryMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Jude Vincent Dobbin Power
- Department of BiochemistryMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Anand Yethiraj
- Department of Physics and Physical OceanographyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Valerie Booth
- Department of BiochemistryMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Department of Physics and Physical OceanographyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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2
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Suárez-Rivero JM, López-Pérez J, Muela-Zarzuela I, Pastor-Maldonado C, Cilleros-Holgado P, Gómez-Fernández D, Álvarez-Córdoba M, Munuera-Cabeza M, Talaverón-Rey M, Povea-Cabello S, Suárez-Carrillo A, Piñero-Pérez R, Reche-López D, Romero-Domínguez JM, Sánchez-Alcázar JA. Neurodegeneration, Mitochondria, and Antibiotics. Metabolites 2023; 13:metabo13030416. [PMID: 36984858 PMCID: PMC10056573 DOI: 10.3390/metabo13030416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Neurodegenerative diseases are characterized by the progressive loss of neurons, synapses, dendrites, and myelin in the central and/or peripheral nervous system. Actual therapeutic options for patients are scarce and merely palliative. Although they affect millions of patients worldwide, the molecular mechanisms underlying these conditions remain unclear. Mitochondrial dysfunction is generally found in neurodegenerative diseases and is believed to be involved in the pathomechanisms of these disorders. Therefore, therapies aiming to improve mitochondrial function are promising approaches for neurodegeneration. Although mitochondrial-targeted treatments are limited, new research findings have unraveled the therapeutic potential of several groups of antibiotics. These drugs possess pleiotropic effects beyond their anti-microbial activity, such as anti-inflammatory or mitochondrial enhancer function. In this review, we will discuss the controversial use of antibiotics as potential therapies in neurodegenerative diseases.
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Affiliation(s)
- Juan M. Suárez-Rivero
- Institute for Biomedical Researching and Innovation of Cádiz (INiBICA) University Hospital Puerta del Mar, 11009 Cádiz, Spain
| | - Juan López-Pérez
- Institute for Biomedical Researching and Innovation of Cádiz (INiBICA) University Hospital Puerta del Mar, 11009 Cádiz, Spain
| | - Inés Muela-Zarzuela
- Institute for Biomedical Researching and Innovation of Cádiz (INiBICA) University Hospital Puerta del Mar, 11009 Cádiz, Spain
| | - Carmen Pastor-Maldonado
- Department of Molecular Biology Interfaculty Institute for Cell Biology, University of Tuebingen, D-72076 Tuebingen, Germany
| | - Paula Cilleros-Holgado
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - David Gómez-Fernández
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - Mónica Álvarez-Córdoba
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - Manuel Munuera-Cabeza
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - Marta Talaverón-Rey
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - Suleva Povea-Cabello
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - Alejandra Suárez-Carrillo
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - Rocío Piñero-Pérez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - Diana Reche-López
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - José M. Romero-Domínguez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
| | - José Antonio Sánchez-Alcázar
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide-University), 41013 Sevilla, Spain
- Correspondence: ; Tel.: +34-954978071
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3
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White DN, Stowell MHB. Room for Two: The Synaptophysin/Synaptobrevin Complex. Front Synaptic Neurosci 2021; 13:740318. [PMID: 34616284 PMCID: PMC8488437 DOI: 10.3389/fnsyn.2021.740318] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/18/2021] [Indexed: 12/01/2022] Open
Abstract
Synaptic vesicle release is regulated by upwards of 30 proteins at the fusion complex alone, but disruptions in any one of these components can have devastating consequences for neuronal communication. Aberrant molecular responses to calcium signaling at the pre-synaptic terminal dramatically affect vesicle trafficking, docking, fusion, and release. At the organismal level, this is reflected in disorders such as epilepsy, depression, and neurodegeneration. Among the myriad pre-synaptic proteins, perhaps the most functionally mysterious is synaptophysin (SYP). On its own, this vesicular transmembrane protein has been proposed to function as a calcium sensor, a cholesterol-binding protein, and to form ion channels across the phospholipid bilayer. The downstream effects of these functions are largely unknown. The physiological relevance of SYP is readily apparent in its interaction with synaptobrevin (VAMP2), an integral element of the neuronal SNARE complex. SNAREs, soluble NSF attachment protein receptors, comprise a family of proteins essential for vesicle fusion. The complex formed by SYP and VAMP2 is thought to be involved in both trafficking to the pre-synaptic membrane as well as regulation of SNARE complex formation. Recent structural observations specifically implicate the SYP/VAMP2 complex in anchoring the SNARE assembly at the pre-synaptic membrane prior to vesicle fusion. Thus, the SYP/VAMP2 complex appears vital to the form and function of neuronal exocytotic machinery.
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Affiliation(s)
- Dustin N. White
- MCD Biology, University of Colorado Boulder, Boulder, CO, United States
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4
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Oganesyan I, Lento C, Tandon A, Wilson DJ. Conformational Dynamics of α-Synuclein during the Interaction with Phospholipid Nanodiscs by Millisecond Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1169-1179. [PMID: 33784451 DOI: 10.1021/jasms.0c00463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Both normal and pathological functions of α-synuclein (αSN), an abundant protein in the central and peripheral nervous system, have been linked to its interaction with membrane lipid bilayers. The ability to characterize structural transitions of αSN upon membrane complexation will clarify molecular mechanisms associated with αSN-linked pathologies, including Parkinson's disease (PD), multiple systems atrophy, and other synucleinopathies. In this work, time-resolved electrospray ionization hydrogen/deuterium exchange mass spectrometry (TRESI-HDX-MS) was employed to acquire a detailed picture of αSN's conformational transitions as it undergoes complexation with nanodisc membrane mimics with different headgroup charges (zwitterionic DMPC and negative POPG). Using this approach, αSN interactions with DMPC nanodiscs were shown to be rapid exchanging and to have little impact on the αSN conformational ensemble. Interactions with nanodiscs containing lipids known to promote amyloidogenesis (e.g., POPG), on the other hand, were observed to induce substantial and specific changes in the αSN conformational ensemble. Ultimately, we identify a region corresponding residues 19-28 and 45-57 of the αSN sequence that is uniquely impacted by interactions with "amyloidogenic" lipid membranes, supporting the existing "broken-helix" model for α-synuclein/membrane interactions, but do not detect a "helical extension" that is also thought to play a role in αSN aggregation.
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Affiliation(s)
- Irina Oganesyan
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Anurag Tandon
- Department of Medicine, University of Toronto, Toronto M5S 1A1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto M3J 1P3, Canada
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5
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Jakubec M, Bariås E, Furse S, Govasli ML, George V, Turcu D, Iashchishyn IA, Morozova-Roche LA, Halskau Ø. Cholesterol-containing lipid nanodiscs promote an α-synuclein binding mode that accelerates oligomerization. FEBS J 2021; 288:1887-1905. [PMID: 32892498 DOI: 10.1111/febs.15551] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 07/28/2020] [Accepted: 09/01/2020] [Indexed: 01/09/2023]
Abstract
Dysregulation of the biosynthesis of cholesterol and other lipids has been implicated in many neurological diseases, including Parkinson's disease. Misfolding of α-synuclein (α-Syn), the main actor in Parkinson's disease, is associated with changes in a lipid environment. However, the exact molecular mechanisms underlying cholesterol effect on α-Syn binding to lipids as well as α-Syn oligomerization and fibrillation remain elusive, as does the relative importance of cholesterol compared to other factors. We probed the interactions and fibrillation behaviour of α-Syn using styrene-maleic acid nanodiscs, containing zwitterionic and anionic lipid model systems with and without cholesterol. Surface plasmon resonance and thioflavin T fluorescence assays were employed to monitor α-Syn binding, as well as fibrillation in the absence and presence of membrane models. 1 H-15 N-correlated NMR was used to monitor the fold of α-Syn in response to nanodisc binding, determining individual residue apparent affinities for the nanodisc-contained bilayers. The addition of cholesterol inhibited α-Syn interaction with lipid bilayers and, however, significantly promoted α-Syn fibrillation, with a more than a 20-fold reduction of lag times before fibrillation onset. When α-Syn bilayer interactions were analysed at an individual residue level by solution-state NMR, we observed two different effects of cholesterol. In nanodiscs made of DOPC, the addition of cholesterol modulated the NAC part of α-Syn, leading to stronger interaction of this region with the lipid bilayer. In contrast, in the nanodiscs comprising DOPC, DOPE and DOPG, the NAC part was mostly unaffected by the presence of cholesterol, while the binding of the N and the C termini was both inhibited.
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Affiliation(s)
- Martin Jakubec
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Espen Bariås
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Samuel Furse
- Department of Molecular Biology, University of Bergen, Norway
| | - Morten L Govasli
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
- Division of Infection and Immunity, University College London, London, UK
| | - Vinnit George
- Department of Chemistry, University of Bergen, Norway
| | - Diana Turcu
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
| | - Igor A Iashchishyn
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | | | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Norway
- Department of Molecular Biology, University of Bergen, Norway
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6
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Dominguez-Meijide A, Parrales V, Vasili E, González-Lizárraga F, König A, Lázaro DF, Lannuzel A, Haik S, Del Bel E, Chehín R, Raisman-Vozari R, Michel PP, Bizat N, Outeiro TF. Doxycycline inhibits α-synuclein-associated pathologies in vitro and in vivo. Neurobiol Dis 2021; 151:105256. [PMID: 33429042 DOI: 10.1016/j.nbd.2021.105256] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are neurodegenerative disorders characterized by the misfolding and aggregation of alpha-synuclein (aSyn). Doxycycline, a tetracyclic antibiotic shows neuroprotective effects, initially proposed to be due to its anti-inflammatory properties. More recently, an additional mechanism by which doxycycline may exert its neuroprotective effects has been proposed as it has been shown that it inhibits amyloid aggregation. Here, we studied the effects of doxycycline on aSyn aggregation in vivo, in vitro and in a cell free system using real-time quaking induced conversion (RT-QuiC). Using H4, SH-SY5Y and HEK293 cells, we found that doxycycline decreases the number and size of aSyn aggregates in cells. In addition, doxycycline inhibits the aggregation and seeding of recombinant aSyn, and attenuates the production of mitochondrial-derived reactive oxygen species. Finally, we found that doxycycline induces a cellular redistribution of aggregates in a C.elegans animal model of PD, an effect that is associated with a recovery of dopaminergic function. In summary, we provide strong evidence that doxycycline treatment may be an effective strategy against synucleinopathies.
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Affiliation(s)
- Antonio Dominguez-Meijide
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany; Laboratory of Neuroanatomy and Experimental Neurology, Dept. of Morphological Sciences, CIMUS, IDIS, University of Santiago de Compostela, Santiago de Compostela, Spain; Networking Research Center on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Valeria Parrales
- Paris Brain Institute, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013 Paris, France
| | - Eftychia Vasili
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany
| | | | - Annekatrin König
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany
| | - Diana F Lázaro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany
| | - Annie Lannuzel
- Paris Brain Institute, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013 Paris, France; University Hospital of Pointe-à-Pitre, Neurology Department, route de Chauvel, 97139 Abymes, Guadeloupe
| | - Stéphane Haik
- Paris Brain Institute, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013 Paris, France; AP-HP, Cellule Nationale de Référence des Maladies de Creutzfeldt-Jakob, University Hospital Pitié-Salpêtrière, Paris F-75013, France
| | - Elaine Del Bel
- Department of Basic and Oral Biology, Faculty of Odontology of Ribeirão Preto, University of São Paulo (USP), Av do Café s/n, São Paulo, Brazil
| | - Rosana Chehín
- Instituto de Investigación en Medicina Molecular y Celular Aplicada (IMMCA) (CONICET-UNT-SIPROSA), Argentina
| | - Rita Raisman-Vozari
- Paris Brain Institute, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013 Paris, France
| | - Patrick P Michel
- Paris Brain Institute, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013 Paris, France
| | - Nicolas Bizat
- Paris Brain Institute, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013 Paris, France; Faculté de Pharmacie de Paris, Paris University, 4 avenue de l'Observatoire, Paris F-75006, France.
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany; Max Planck Institute for Experimental Medicine, Goettingen, Germany; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, UK.
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7
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Fatafta H, Samantray S, Sayyed-Ahmad A, Coskuner-Weber O, Strodel B. Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:135-185. [PMID: 34656328 DOI: 10.1016/bs.pmbts.2021.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce metadynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
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Affiliation(s)
- Hebah Fatafta
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Suman Samantray
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; AICES Graduate School, RWTH Aachen University, Aachen, Germany
| | | | - Orkid Coskuner-Weber
- Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi, Istanbul, Turkey
| | - Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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8
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Jurczak P, Sikorska E, Czaplewska P, Rodziewicz-Motowidlo S, Zhukov I, Szymanska A. The Influence of the Mixed DPC:SDS Micelle on the Structure and Oligomerization Process of the Human Cystatin C. MEMBRANES 2020; 11:17. [PMID: 33374409 PMCID: PMC7824358 DOI: 10.3390/membranes11010017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/23/2022]
Abstract
Human cystatin C (hCC), a member of the superfamily of papain-like cysteine protease inhibitors, is the most widespread cystatin in human body fluids. Physiologically active hCC is a monomer, which dimerization and oligomerization lead to the formation of the inactive, insoluble amyloid form of the protein, strictly associated with cerebral amyloid angiopathy, a severe state causing death among young patients. It is known, that biological membranes may accelerate the oligomerization processes of amyloidogenic proteins. Therefore, in this study, we describe an influence of membrane mimetic environment-mixed dodecylphosphocholine:sodium dodecyl sulfate (DPC:SDS) micelle (molar ratio 5:1)-on the effect of the hCC oligomerization. The hCC-micelle interactions were analyzed with size exclusion chromatography, circular dichroism, and nuclear magnetic resonance spectroscopy. The experiments were performed on the wild-type (WT) cystatin C, and two hCC variants-V57P and V57G. Collected experimental data were supplemented with molecular dynamic simulations, making it possible to highlight the binding interface and select the residues involved in interactions with the micelle. Obtained data shows that the mixed DPC:SDS micelle does not accelerate the oligomerization of protein and even reverses the hCC dimerization process.
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Affiliation(s)
- Przemyslaw Jurczak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (E.S.); (S.R.-M.)
| | - Emilia Sikorska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (E.S.); (S.R.-M.)
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG & MUG, University of Gdańsk, Gdańsk, Abrahama 58, 80-307 Gdańsk, Poland;
| | | | - Igor Zhukov
- NanoBioMedical Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Aneta Szymanska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (E.S.); (S.R.-M.)
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9
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Klöpfer K, Hagn F. Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:271-283. [PMID: 31779883 DOI: 10.1016/j.pnmrs.2019.08.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.
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Affiliation(s)
- Kai Klöpfer
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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10
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Yeboah F, Kim TE, Bill A, Dettmer U. Dynamic behaviors of α-synuclein and tau in the cellular context: New mechanistic insights and therapeutic opportunities in neurodegeneration. Neurobiol Dis 2019; 132:104543. [PMID: 31351173 DOI: 10.1016/j.nbd.2019.104543] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022] Open
Abstract
α-Synuclein (αS) and tau have a lot in common. Dyshomeostasis and aggregation of both proteins are central in the pathogenesis of neurodegenerative diseases: Parkinson's disease, dementia with Lewy bodies, multi-system atrophy and other 'synucleinopathies' in the case of αS; Alzheimer's disease, frontotemporal dementia, progressive supranuclear palsy and other 'tauopathies' in the case of tau. The aggregated states of αS and tau are found to be (hyper)phosphorylated, but the relevance of the phosphorylation in health or disease is not well understood. Both tau and αS are typically characterized as 'intrinsically disordered' proteins, while both engage in transient interactions with cellular components, thereby undergoing structural changes and context-specific folding. αS transiently binds to (synaptic) vesicles forming a membrane-induced amphipathic helix; tau transiently interacts with microtubules forming an 'extended structure'. The regulation and exact nature of the interactions are not fully understood. Here we review recent and previous insights into the dynamic, transient nature of αS and tau with regard to the mode of interaction with their targets, the dwell-time while bound, and the cis and trans factors underlying the frequent switching between bound and unbound states. These aspects are intimately linked to hypotheses on how subtle changes in the transient behaviors may trigger the earliest steps in the pathogenesis of the respective brain diseases. Based on a deeper understanding of transient αS and tau conformations in the cellular context, new therapeutic strategies may emerge, and it may become clearer why existing approaches have failed or how they could be optimized.
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Affiliation(s)
- Fred Yeboah
- Novartis Institute for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, MA 02139, USA
| | - Tae-Eun Kim
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Anke Bill
- Novartis Institute for Biomedical Research, Chemical Biology and Therapeutics, Cambridge, MA 02139, USA.
| | - Ulf Dettmer
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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Adnan M, Islam W, Zhang J, Zheng W, Lu GD. Diverse Role of SNARE Protein Sec22 in Vesicle Trafficking, Membrane Fusion, and Autophagy. Cells 2019; 8:E337. [PMID: 30974782 PMCID: PMC6523435 DOI: 10.3390/cells8040337] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/02/2019] [Accepted: 04/05/2019] [Indexed: 01/09/2023] Open
Abstract
Protein synthesis begins at free ribosomes or ribosomes attached with the endoplasmic reticulum (ER). Newly synthesized proteins are transported to the plasma membrane for secretion through conventional or unconventional pathways. In conventional protein secretion, proteins are transported from the ER lumen to Golgi lumen and through various other compartments to be secreted at the plasma membrane, while unconventional protein secretion bypasses the Golgi apparatus. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE) proteins are involved in cargo vesicle trafficking and membrane fusion. The ER localized vesicle associated SNARE (v-SNARE) protein Sec22 plays a major role during anterograde and retrograde transport by promoting efficient membrane fusion and assisting in the assembly of higher order complexes by homodimer formation. Sec22 is not only confined to ER-Golgi intermediate compartments (ERGIC) but also facilitates formation of contact sites between ER and plasma membranes. Sec22 mutation is responsible for the development of atherosclerosis and symptoms in the brain in Alzheimer's disease and aging in humans. In the fruit fly Drosophila melanogaster, Sec22 is essential for photoreceptor morphogenesis, the wingless signaling pathway, and normal ER, Golgi, and endosome morphology. In the plant Arabidopsis thaliana, it is involved in development, and in the nematode Caenorhabditis elegans, it is in involved in the RNA interference (RNAi) pathway. In filamentous fungi, it affects cell wall integrity, growth, reproduction, pathogenicity, regulation of reactive oxygen species (ROS), expression of extracellular enzymes, and transcriptional regulation of many development related genes. This review provides a detailed account of Sec22 function, summarizes its domain structure, discusses its genetic redundancy with Ykt6, discusses what is known about its localization to discrete membranes, its contributions in conventional and unconventional autophagy, and a variety of other roles across different cellular systems ranging from higher to lower eukaryotes, and highlights some of the surprises that have originated from research on Sec22.
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Affiliation(s)
- Muhammad Adnan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Waqar Islam
- College of Geographical Sciences, Fujian Normal University, Fuzhou 350007, Fujian, China.
| | - Jing Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Guo-Dong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, and Key Laboratory of Bio-pesticides and Chemical Biology Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Isotopic Labeling of Eukaryotic Membrane Proteins for NMR Studies of Interactions and Dynamics. Methods Enzymol 2018; 614:37-65. [PMID: 30611431 DOI: 10.1016/bs.mie.2018.08.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Membrane proteins, and especially G-protein coupled receptors (GPCRs), are increasingly important targets of structural biology studies due to their involvement in many biomedically critical pathways in humans. These proteins are often highly dynamic and thus benefit from studies by NMR spectroscopy in parallel with complementary crystallographic and cryo-EM analyses. However, such studies are often complicated by a range of practical concerns, including challenges in preparing suitably isotopically labeled membrane protein samples, large sizes of protein/detergent or protein/lipid complexes, and limitations on sample concentrations and stabilities. Here we describe our approach to addressing these challenges via the use of simple eukaryotic expression systems and modified NMR experiments, using the human adenosine A2A receptor as an example. Protocols are provided for the preparation of U-2H (13C,1H-Ile δ1)-labeled membrane proteins from overexpression in the methylotrophic yeast Pichia pastoris, as well as techniques for studying the fast ns-ps sidechain dynamics of the methyl groups of such samples. We believe that, with the proper optimization, these protocols should be generalizable to other GPCRs and human membrane proteins.
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