1
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Wieczorek P, Jarmołowski A, Szweykowska-Kulińska Z, Kozak M, Taube M. Solution structure and behaviour of the Arabidopsis thaliana HYL1 protein. Biochim Biophys Acta Gen Subj 2023; 1867:130376. [PMID: 37150226 DOI: 10.1016/j.bbagen.2023.130376] [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: 01/30/2023] [Revised: 04/14/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
In plants, microRNA biogenesis involves the complex assembly of molecular processes that are mostly governed by three proteins: RNase III protein DCL1 and two RNA binding proteins, SERRATE and HYL1. HYL1 protein is a double stranded RNA binding protein that is needed for the precise excision of miRNA/miRNA* duplex from the stem-loop containing primary miRNA gene transcripts. Moreover, HYL1 protein partners with HSP90 and CARP9 proteins to load the miRNA molecules onto the AGO1 endonuclease. HYL1 protein as a crucial player in the biogenesis pathway is regulated by its phosphorylation status to fine tune the levels of miRNA in various physiological conditions. HYL1 protein consists of two dsRNA binding domains (dsRBD) that are involved in RNA binding and dimerization and a C-terminal disordered tail of unknown function. Although the spatial structures of the individual dsRBDs have been determined there is a lack of information about the behaviour and structure of the full length protein. Using small the angle X-ray scattering (SAXS) technique we investigated the structure and dynamic of the HYL1 protein from Arabidopsis thaliana in solution. We show that the C-terminal domain is disordered and dynamic in solution and that HYL1 protein dimerization is dependent on the concentration. HYL1 protein lacking a C-terminal tail and a nuclear localisation signal (NLS) fragment is almost exclusively monomeric and similarly to full-length protein has a dynamic nature in solution. Our results point for the first time to the role of the C-terminal fragment in stabilisation of HYL1 dimer formation.
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Affiliation(s)
- Przemysław Wieczorek
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Artur Jarmołowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Maciej Kozak
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland
| | - Michał Taube
- Department of Biomedical Physics, Institute of Physics, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614 Poznań, Poland.
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2
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Zamel J, Chen J, Zaer S, Harris PD, Drori P, Lebendiker M, Kalisman N, Dokholyan NV, Lerner E. Structural and dynamic insights into α-synuclein dimer conformations. Structure 2023; 31:411-423.e6. [PMID: 36809765 PMCID: PMC10081966 DOI: 10.1016/j.str.2023.01.011] [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: 11/20/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/22/2023]
Abstract
Parkinson disease is associated with the aggregation of the protein α-synuclein. While α-synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate that α-synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers, we identify one that is compact, stable, abundant, and exhibits partially exposed β-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in proximity that may promote dityrosine covalent linkage upon hydroxyl radicalization, which is implicated in α-synuclein amyloid fibrils. We propose that this α-synuclein dimer features etiological relevance to Parkinson disease.
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Affiliation(s)
- Joanna Zamel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Sofia Zaer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paul David Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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3
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Langkilde AE, Vestergaard B. Protein fibrillation from another small angle-SAXS data analysis of developing systems. Methods Enzymol 2022; 678:377-409. [PMID: 36641215 DOI: 10.1016/bs.mie.2022.09.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the fibrillation process amyloid proteins undergo structural changes at very different length and time scales. Small angle X-ray scattering (SAXS) is a method that is uniquely suitable for the structural analysis of this process. Careful measures must, however, be taken both in the sample preparation, data collection and data analysis procedures to ensure proper data quality, coverage of the process and reliable interpretation. With this chapter, we provide many details about the data analysis of such developing systems. The recommendations are based on our own experience with analysis of data from several amyloid and amyloid-like proteins, with data decomposition being a central point in the procedure. We focus on two alternative approaches, one being a laborious, hands-on, iterative approach, the other being more automated, applying a chemometrics based software, developed for the purpose. Both methods can equally well be applied to other developing mixtures, but specific recommendations for amyloid samples are emphasized in this chapter.
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Affiliation(s)
- Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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4
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Sahin C, Østerlund EC, Österlund N, Costeira-Paulo J, Pedersen JN, Christiansen G, Nielsen J, Grønnemose AL, Amstrup SK, Tiwari MK, Rao RSP, Bjerrum MJ, Ilag LL, Davies MJ, Marklund EG, Pedersen JS, Landreh M, Møller IM, Jørgensen TJD, Otzen DE. Structural Basis for Dityrosine-Mediated Inhibition of α-Synuclein Fibrillization. J Am Chem Soc 2022; 144:11949-11954. [PMID: 35749730 PMCID: PMC9284551 DOI: 10.1021/jacs.2c03607] [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] [Indexed: 11/29/2022]
Abstract
![]()
α-Synuclein
(α-Syn) is an intrinsically disordered
protein which self-assembles into highly organized β-sheet structures
that accumulate in plaques in brains of Parkinson’s disease
patients. Oxidative stress influences α-Syn structure and self-assembly;
however, the basis for this remains unclear. Here we characterize
the chemical and physical effects of mild oxidation on monomeric α-Syn
and its aggregation. Using a combination of biophysical methods, small-angle
X-ray scattering, and native ion mobility mass spectrometry, we find
that oxidation leads to formation of intramolecular dityrosine cross-linkages
and a compaction of the α-Syn monomer by a factor of √2.
Oxidation-induced compaction is shown to inhibit ordered self-assembly
and amyloid formation by steric hindrance, suggesting an important
role of mild oxidation in preventing amyloid formation.
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Affiliation(s)
- Cagla Sahin
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Eva Christina Østerlund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, SE-114 18 Stockholm, Sweden
| | - Joana Costeira-Paulo
- Department of Chemistry - BMC, BMC - Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Gunna Christiansen
- Department of Health Science and Technology, Medical Microbiology and Immunology, Aalborg University, Fredrik Bajers Vej 3b, DK-9220 Aalborg Ø, Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Anne Louise Grønnemose
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Søren Kirk Amstrup
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - Manish K Tiwari
- Department Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangaluru-575018, Karnataka, India
| | - Morten Jannik Bjerrum
- Department Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Leopold L Ilag
- Department of Materials and Environmental Chemistry, Stockholm University, SE-114 18 Stockholm, Sweden
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Erik G Marklund
- Department of Chemistry - BMC, BMC - Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 65 Solna, Sweden
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
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5
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Vestergaard B, Langkilde AE. Protein fibrillation from another small angle: Sample preparation and SAXS data collection. Methods Enzymol 2022; 677:291-321. [DOI: 10.1016/bs.mie.2022.08.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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6
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Modification of Glyceraldehyde-3-Phosphate Dehydrogenase with Nitric Oxide: Role in Signal Transduction and Development of Apoptosis. Biomolecules 2021; 11:biom11111656. [PMID: 34827652 PMCID: PMC8615796 DOI: 10.3390/biom11111656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 01/07/2023] Open
Abstract
This review focuses on the consequences of GAPDH S-nitrosylation at the catalytic cysteine residue. The widespread hypothesis according to which S-nitrosylation causes a change in GAPDH structure and its subsequent binding to the Siah1 protein is considered in detail. It is assumed that the GAPDH complex with Siah1 is transported to the nucleus by carrier proteins, interacts with nuclear proteins, and induces apoptosis. However, there are several conflicting and unproven elements in this hypothesis. In particular, there is no direct confirmation of the interaction between the tetrameric GAPDH and Siah1 caused by S-nitrosylation of GAPDH. The question remains as to whether the translocation of GAPDH into the nucleus is caused by S-nitrosylation or by some other modification of the catalytic cysteine residue. The hypothesis of the induction of apoptosis by oxidation of GAPDH is considered. This oxidation leads to a release of the coenzyme NAD+ from the active center of GAPDH, followed by the dissociation of the tetramer into subunits, which move to the nucleus due to passive transport and induce apoptosis. In conclusion, the main tasks are summarized, the solutions to which will make it possible to more definitively establish the role of nitric oxide in the induction of apoptosis.
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7
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Megadalton-sized Dityrosine Aggregates of α-Synuclein Retain High Degrees of Structural Disorder and Internal Dynamics. J Mol Biol 2020; 432:166689. [PMID: 33211011 PMCID: PMC7779668 DOI: 10.1016/j.jmb.2020.10.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Despite their large size, αSyn dityrosine aggregates are dynamic and disordered. αSyn dityrosine aggregates specifically form in complex environments. αSyn dityrosine aggregates retain residual membrane binding activity. Dityrosine aggregates inhibit amyloid formation of monomeric αSyn. αSyn dityrosine aggregates are not cytotoxic.
Heterogeneous aggregates of the human protein α-synuclein (αSyn) are abundantly found in Lewy body inclusions of Parkinson’s disease patients. While structural information on classical αSyn amyloid fibrils is available, little is known about the conformational properties of disease-relevant, non-canonical aggregates. Here, we analyze the structural and dynamic properties of megadalton-sized dityrosine adducts of αSyn that form in the presence of reactive oxygen species and cytochrome c, a proapoptotic peroxidase that is released from mitochondria during sustained oxidative stress. In contrast to canonical cross-β amyloids, these aggregates retain high degrees of internal dynamics, which enables their characterization by solution-state NMR spectroscopy. We find that intermolecular dityrosine crosslinks restrict αSyn motions only locally whereas large segments of concatenated molecules remain flexible and disordered. Indistinguishable aggregates form in crowded in vitro solutions and in complex environments of mammalian cell lysates, where relative amounts of free reactive oxygen species, rather than cytochrome c, are rate limiting. We further establish that dityrosine adducts inhibit classical amyloid formation by maintaining αSyn in its monomeric form and that they are non-cytotoxic despite retaining basic membrane-binding properties. Our results suggest that oxidative αSyn aggregation scavenges cytochrome c’s activity into the formation of amorphous, high molecular-weight structures that may contribute to the structural diversity of Lewy body deposits.
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8
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Skaanning LK, Santoro A, Skamris T, Martinsen JH, D’Ursi AM, Bucciarelli S, Vestergaard B, Bugge K, Langkilde AE, Kragelund BB. The Non-Fibrillating N-Terminal of α-Synuclein Binds and Co-Fibrillates with Heparin. Biomolecules 2020; 10:E1192. [PMID: 32824376 PMCID: PMC7464290 DOI: 10.3390/biom10081192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 01/16/2023] Open
Abstract
The intrinsically disordered protein α-synuclein (aSN) is, in its fibrillated state, the main component of Lewy bodies-hallmarks of Parkinson's disease. Additional Lewy body components include glycosaminoglycans, including heparan sulfate proteoglycans. In humans, heparan sulfate has, in an age-dependent manner, shown increased levels of sulfation. Heparin, a highly sulfated glycosaminoglycan, is a relevant mimic for mature heparan sulfate and has been shown to influence aSN fibrillation. Here, we decompose the underlying properties of the interaction between heparin and aSN and the effect of heparin on fibrillation. Via the isolation of the first 61 residues of aSN, which lacked intrinsic fibrillation propensity, fibrillation could be induced by heparin, and access to the initial steps in fibrillation was possible. Here, structural changes with shifts from disorder via type I β-turns to β-sheets were revealed, correlating with an increase in the aSN1-61/heparin molar ratio. Fluorescence microscopy revealed that heparin and aSN1-61 co-exist in the final fibrils. We conclude that heparin can induce the fibrillation of aSN1-61, through binding to the N-terminal with an affinity that is higher in the truncated form of aSN. It does so by specifically modulating the structure of aSN via the formation of type I β-turn structures likely critical for triggering aSN fibrillation.
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Affiliation(s)
- Line K. Skaanning
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark; (L.K.S.); (T.S.); (J.H.M.); (S.B.); (B.V.)
| | - Angelo Santoro
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark; (A.S.); (K.B.)
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy;
| | - Thomas Skamris
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark; (L.K.S.); (T.S.); (J.H.M.); (S.B.); (B.V.)
| | - Jacob Hertz Martinsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark; (L.K.S.); (T.S.); (J.H.M.); (S.B.); (B.V.)
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark; (A.S.); (K.B.)
| | - Anna Maria D’Ursi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy;
| | - Saskia Bucciarelli
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark; (L.K.S.); (T.S.); (J.H.M.); (S.B.); (B.V.)
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark; (L.K.S.); (T.S.); (J.H.M.); (S.B.); (B.V.)
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark; (A.S.); (K.B.)
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark; (L.K.S.); (T.S.); (J.H.M.); (S.B.); (B.V.)
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark; (A.S.); (K.B.)
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9
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Fricano A, Librizzi F, Rao E, Alfano C, Vetri V. Blue autofluorescence in protein aggregates “lighted on” by UV induced oxidation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140258. [DOI: 10.1016/j.bbapap.2019.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 11/27/2022]
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10
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Lothian A, Lago L, Mukherjee S, Connor AR, Fowler C, McLean CA, Horne M, Masters CL, Cappai R, Roberts BR. Characterization of the metal status of natively purified alpha-synuclein from human blood, brain tissue, or recombinant sources using size exclusion ICP-MS reveals no significant binding of Cu, Fe or Zn. Metallomics 2019; 11:128-140. [DOI: 10.1039/c8mt00223a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The binding of Cu, Fe or Zn to alpha-synuclein has been implicated in neurodegenerative disease, such as Parkinson's.
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Affiliation(s)
- Amber Lothian
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
| | - Larissa Lago
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
| | - Soumya Mukherjee
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
| | - Andrea R. Connor
- Department of Pathology
- The University of Melbourne
- Parkville
- Australia
| | - Chris Fowler
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
| | - Catriona A. McLean
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
- Department of Anatomical Pathology
| | - Malcolm Horne
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
| | - Colin L. Masters
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
| | - Roberto Cappai
- Department of Pathology
- The University of Melbourne
- Parkville
- Australia
- Department of Pharmacology and Therapeutics
| | - Blaine R. Roberts
- The Florey Institute of Neuroscience and Mental Health
- University of Melbourne
- Parkville 3052
- Australia
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11
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Wördehoff MM, Shaykhalishahi H, Groß L, Gremer L, Stoldt M, Buell AK, Willbold D, Hoyer W. Opposed Effects of Dityrosine Formation in Soluble and Aggregated α-Synuclein on Fibril Growth. J Mol Biol 2017; 429:3018-3030. [PMID: 28918091 PMCID: PMC5637163 DOI: 10.1016/j.jmb.2017.09.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/03/2017] [Accepted: 09/06/2017] [Indexed: 12/20/2022]
Abstract
Parkinson's disease is the second most common neurodegenerative disease. It is characterized by aggregation of the protein α-synuclein (α-syn) in Lewy bodies, mitochondrial dysfunction, and increased oxidative stress in the substantia nigra. Oxidative stress leads to several modifications of biomolecules including dityrosine (DiY) crosslinking in proteins, which has recently been detected in α-syn in Lewy bodies from Parkinson's disease patients. Here we report that α-syn is highly susceptible to ultraviolet-induced DiY formation. We investigated DiY formation of α-syn and nine tyrosine-to-alanine mutants and monitored its effect on α-syn fibril formation in vitro. Ultraviolet irradiation of intrinsically disordered α-syn generates DiY-modified monomers and dimers, which inhibit fibril formation of unmodified α-syn by interfering with fibril elongation. The inhibition depends on both the DiY group and its integration into α-syn. When preformed α-syn fibrils are crosslinked by DiY formation, they gain increased resistance to denaturation. DiY-stabilized α-syn fibrils retain their high seeding efficiency even after being exposed to denaturant concentrations that completely depolymerize non-crosslinked seeds. Oxidative stress-associated DiY crosslinking of α-syn therefore entails two opposing effects: (i) inhibition of aggregation by DiY-modified monomers and dimers, and (ii) stabilization of fibrillar aggregates against potential degradation mechanisms, which can lead to promotion of aggregation, especially in the presence of secondary nucleation.
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Affiliation(s)
- Michael M Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Luca Groß
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Lothar Gremer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Matthias Stoldt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Alexander K Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Complex Systems (ICS-6), Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.
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12
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Trabjerg E, Kartberg F, Christensen S, Rand KD. Conformational characterization of nerve growth factor-β reveals that its regulatory pro-part domain stabilizes three loop regions in its mature part. J Biol Chem 2017; 292:16665-16676. [PMID: 28798232 DOI: 10.1074/jbc.m117.803320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/07/2017] [Indexed: 11/06/2022] Open
Abstract
Nerve growth factor-β (NGF) is essential for the correct development of the nervous system. NGF exists in both a mature form and a pro-form (proNGF). The two forms have opposing effects on neurons: NGF induces proliferation, whereas proNGF induces apoptosis via binding to a receptor complex of the common neurotrophin receptor (p75NTR) and sortilin. The overexpression of both proNGF and sortilin has been associated with several neurodegenerative diseases. Insights into the conformational differences between proNGF and NGF are central to a better understanding of the opposing mechanisms of action of NGF and proNGF on neurons. However, whereas the structure of NGF has been determined by X-ray crystallography, the structural details for proNGF remain elusive. Here, using a sensitive MS-based analytical method to measure the hydrogen/deuterium exchange of proteins in solution, we analyzed the conformational properties of proNGF and NGF. We detected the presence of a localized higher-order structure motif in the pro-part of proNGF. Furthermore, by comparing the hydrogen/deuterium exchange in the mature part of NGF and proNGF, we found that the presence of the pro-part in proNGF causes a structural stabilization of three loop regions in the mature part, possibly through a direct molecular interaction. Moreover, using tandem MS analyses, we identified two N-linked and two O-linked glycosylations in the pro-part of proNGF. These results advance our knowledge of the conformational properties of proNGF and NGF and help provide a rationale for the diverse biological effects of NGF and proNGF at the molecular level.
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Affiliation(s)
- Esben Trabjerg
- From the Department of Pharmacy, University of Copenhagen, 2100 Copenhagen E, Denmark and.,the Department of Biologics, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Fredrik Kartberg
- the Department of Biologics, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Søren Christensen
- the Department of Biologics, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Kasper D Rand
- From the Department of Pharmacy, University of Copenhagen, 2100 Copenhagen E, Denmark and
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A simple sheathless CE-MS interface with a sub-micrometer electrical contact fracture for sensitive analysis of peptide and protein samples. Anal Chim Acta 2016; 936:157-67. [PMID: 27566351 DOI: 10.1016/j.aca.2016.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
Online coupling of capillary electrophoresis (CE) to electrospray ionization mass spectrometry (MS) has shown considerable potential, however, technical challenges have limited its use. In this study, we have developed a simple and sensitive sheathless CE-MS interface based on the novel concept of forming a sub-micrometer fracture directly in the capillary. The simple interface design allowed the generation of a stable ESI spray capable of ionization at low nanoliter flow-rates (45-90 nL/min) for high sensitivity MS analysis of challenging samples like those containing proteins and peptides. By analysis of a model peptide (leucine enkephalin), a limit of detection (LOD) of 0.045 pmol/μL (corresponding to 67 attomol in a sample volume of ∼15 nL) was obtained. The merit of the CE-MS approach was demonstrated by analysis of bovine serum albumin (BSA) tryptic peptides. A well-resolved separation profile was achieved and comparable sequence coverage was obtained by the CE-MS method (73%) compared to a representative UPLC-MS method (77%). The CE-MS interface was subsequently used to analyse a more complex sample of pharmaceutically relevant human proteins including insulin, tissue factor and α-synuclein. Efficient separation and protein ESI mass spectra of adequate quality could be achieved using only a small amount of sample (30 fmol). In addition, analysis of ubiquitin samples under both native and denatured conditions, indicate that the CE-MS setup can facilitate native MS applications to probe the conformational properties of proteins. Thus, the described CE-MS setup should be useful for a wide range of high-sensitivity applications in protein research.
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Vestergaard B. Analysis of biostructural changes, dynamics, and interactions – Small-angle X-ray scattering to the rescue. Arch Biochem Biophys 2016; 602:69-79. [DOI: 10.1016/j.abb.2016.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/17/2016] [Accepted: 02/26/2016] [Indexed: 12/27/2022]
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