1
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Lin X, Mandal S, Nithun RV, Kolla R, Bouri B, Lashuel HA, Jbara M. A Versatile Method for Site-Specific Chemical Installation of Aromatic Posttranslational Modification Analogs into Proteins. J Am Chem Soc 2024; 146:25788-25798. [PMID: 39224092 PMCID: PMC11421021 DOI: 10.1021/jacs.4c08416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/23/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Posttranslational modifications (PTMs) of proteins play central roles in regulating the protein structure, interactome, and functions. A notable modification site is the aromatic side chain of Tyr, which undergoes modifications such as phosphorylation and nitration. Despite the biological and physiological importance of Tyr-PTMs, our current understanding of the mechanisms by which these modifications contribute to human health and disease remains incomplete. This knowledge gap arises from the absence of natural amino acids that can mimic these PTMs and the lack of synthetic tools for the site-specific introduction of aromatic PTMs into proteins. Herein, we describe a facile method for the site-specific chemical installation of aromatic PTMs into proteins through palladium-mediated S-C(sp2) bond formation under ambient conditions. We demonstrate the incorporation of novel PTMs such as Tyr-nitration and phosphorylation analogs to synthetic and recombinantly expressed Cys-containing peptides and proteins within minutes and in good yields. To demonstrate the versatility of our approach, we employed it to prepare 10 site-specifically modified proteins, including nitrated and phosphorylated analogs of Myc and Max proteins. Furthermore, we prepared a focused library of site-specifically nitrated and phosphorylated α-synuclein (α-Syn) protein, which enabled, for the first time, deciphering the role of these competing modifications in regulating α-Syn conformation aggregation in vitro. Our strategy offers advantages over synthetic or semisynthetic approaches, as it enables rapid and selective transfer of rarely explored aromatic PTMs into recombinant proteins, thus facilitating the generation of novel libraries of homogeneous posttranslationally modified proteins for biomarker discovery, mechanistic studies, and drug discovery.
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Affiliation(s)
- Xiaoxi Lin
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shaswati Mandal
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Raj V. Nithun
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rajasekhar Kolla
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Bouchra Bouri
- Protein
Production and Structure core facility, School of Life Sciences, École Polytechnique Fédérale
de Lausanne, Lausanne CH-1015, Switzerland
| | - Hilal A. Lashuel
- Laboratory
of Molecular and Chemical Biology of Neurodegeneration, Institute
of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Muhammad Jbara
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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2
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Mancinelli CD, Marx DC, Gonzalez-Hernandez AJ, Huynh K, Mancinelli L, Arefin A, Khelashvilli G, Levitz J, Eliezer D. Control of G protein-coupled receptor function via membrane-interacting intrinsically disordered C-terminal domains. Proc Natl Acad Sci U S A 2024; 121:e2407744121. [PMID: 38985766 PMCID: PMC11260148 DOI: 10.1073/pnas.2407744121] [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: 04/29/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
G protein-coupled receptors (GPCRs) control intracellular signaling cascades via agonist-dependent coupling to intracellular transducers including heterotrimeric G proteins, GPCR kinases (GRKs), and arrestins. In addition to their critical interactions with the transmembrane core of active GPCRs, all three classes of transducers have also been reported to interact with receptor C-terminal domains (CTDs). An underexplored aspect of GPCR CTDs is their possible role as lipid sensors given their proximity to the membrane. CTD-membrane interactions have the potential to control the accessibility of key regulatory CTD residues to downstream effectors and transducers. Here, we report that the CTDs of two closely related family C GPCRs, metabotropic glutamate receptor 2 (mGluR2) and mGluR3, bind to membranes and that this interaction can regulate receptor function. We first characterize CTD structure with NMR spectroscopy, revealing lipid composition-dependent modes of membrane binding. Using molecular dynamics simulations and structure-guided mutagenesis, we then identify key conserved residues and cancer-associated mutations that modulate CTD-membrane binding. Finally, we provide evidence that mGluR3 transducer coupling is controlled by CTD-membrane interactions in live cells, which may be subject to regulation by CTD phosphorylation and changes in membrane composition. This work reveals an additional mechanism of GPCR modulation, suggesting that CTD-membrane binding may be a general regulatory mode throughout the broad GPCR superfamily.
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Affiliation(s)
| | - Dagan C. Marx
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
| | | | - Kevin Huynh
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
| | - Lucia Mancinelli
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
| | - Anisul Arefin
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
| | - George Khelashvilli
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY10065
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Department of Psychiatry, Weill Cornell Medicine, New York, NY10065
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY10065
- Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY10065
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3
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Gatzemeier LM, Meyer F, Outeiro TF. Synthesis and Semi-Synthesis of Alpha-Synuclein: Insight into the Chemical Complexity of Synucleinopathies. Chembiochem 2024:e202400253. [PMID: 38965889 DOI: 10.1002/cbic.202400253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/06/2024]
Abstract
The chemical rules governing protein folding have intrigued generations of researchers for decades. With the advent of artificial intelligence (AI), prediction of protein structure has improved tremendously. However, there is still a level of analysis that is only possible through wet laboratory experiments, especially in respect to the investigation of the pathological effect of mutations and posttranslational modifications (PTMs) on proteins of interest. This requires the availability of pure peptides and proteins in sufficient quantities for biophysical, biochemical, and functional studies. In this context, chemical protein synthesis and semi-synthesis are powerful tools in protein research, which help to enlighten the role of protein modification in the physiology and pathology of proteins. A protein of high interest in the field of biomedicine is alpha-synuclein (aSyn), a protein deeply associated with several devastating neurodegenerative disorders such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), or multiple systems atrophy (MSA). Here, we describe several methods and pathways to synthesize native or modified aSyn, and discuss how these approaches enable us to address pathological mechanisms that may open novel perspectives for therapeutic intervention.
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Affiliation(s)
- Luisa Maria Gatzemeier
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany
| | - Franc Meyer
- Institute of Inorganic Chemistry, University of Göttingen, Tammannstraße 4, 37077, Göttingen, Germany
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Waldweg 33, 37073, Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Straße 3, 37075, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, United Kingdom
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Von Siebold-Straße 3a, 37075, Göttingen, Germany
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4
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Mancinelli C, Marx DC, Gonzalez-Hernandez AJ, Huynh K, Mancinelli L, Arefin A, Khelashvilli G, Levitz J, Eliezer D. Control of G protein-coupled receptor function via membrane-interacting intrinsically disordered C-terminal domains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.16.553551. [PMID: 37645938 PMCID: PMC10462050 DOI: 10.1101/2023.08.16.553551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
G protein-coupled receptors (GPCRs) control intracellular signaling cascades via agonist-dependent coupling to intracellular transducers including heterotrimeric G proteins, GPCR kinases (GRKs), and arrestins. In addition to their critical interactions with the transmembrane core of active GPCRs, all three classes of transducers have also been reported to interact with receptor C-terminal domains (CTDs). An underexplored aspect of GPCR CTDs is their possible role as lipid sensors given their proximity to the membrane. CTD-membrane interactions have the potential to control the accessibility of key regulatory CTD residues to downstream effectors and transducers. Here we report that the CTDs of two closely related family C GPCRs, metabotropic glutamate receptor 2 (mGluR2) and mGluR3, bind to membranes and that this interaction can regulate receptor function. We first characterize CTD structure with NMR spectroscopy, revealing lipid composition-dependent modes of membrane binding. Using molecular dynamics simulations and structure-guided mutagenesis, we then identify key conserved residues and cancer-associated mutations that modulate CTD-membrane binding. Finally, we provide evidence that mGluR3 transducer coupling is controlled by CTD-membrane interactions in live cells, which may be subject to regulation by CTD phosphorylation and changes in membrane composition. This work reveals a novel mechanism of GPCR modulation, suggesting that CTD-membrane binding may be a general regulatory mode throughout the broad GPCR superfamily.
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Affiliation(s)
- Chiara Mancinelli
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
- equal contribution
| | - Dagan C. Marx
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
- equal contribution
| | | | - Kevin Huynh
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lucia Mancinelli
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anisul Arefin
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - George Khelashvilli
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Psychiatry, Weill Cornell Medicine, New York, NY 10065, USA
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
- Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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5
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Kapila S, Sun Y, Peng C, Zhang S. Soluble alpha-synuclein post-translational modifications: unexpected regulators of pathological alpha-synuclein amplification. Neural Regen Res 2024; 19:959-960. [PMID: 37862188 PMCID: PMC10749622 DOI: 10.4103/1673-5374.385303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/05/2023] [Accepted: 07/26/2023] [Indexed: 10/22/2023] Open
Affiliation(s)
- Simran Kapila
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Yuhan Sun
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chao Peng
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, Brain Research Institute, Mary S. Easton Center for Alzheimer’s Research, University of California, Los Angeles, CA, USA
| | - Shujing Zhang
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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6
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Abstract
Deposits of the microtubule-associated protein Tau (MAPT) serve as a hallmark of neurodegenerative diseases known as tauopathies. Numerous studies have demonstrated that in diseases such as Alzheimer's disease (AD), Tau undergoes extensive remodeling. The attachment of post-translational modifications distributed throughout the entire sequence of the protein correlates with clinical presentation. A systematic examination of these protein alterations can shed light on their roles in both healthy and diseased states. However, the ability to access these modifications in the entire protein chain is limited as Tau can only be produced recombinantly or through semisynthesis. In this article, we describe the first chemical synthesis of the longest 2N4R isoform of Tau, consisting of 441 amino acids. The 2N4R Tau was divided into 3 major segments and a total of 11 fragments, all of which were prepared via solid-phase peptide synthesis. The successful chemical strategy has relied on the strategic use of two cysteine sites (C291 and C322) for the native chemical ligations (NCLs). This was combined with modern preparative protein chemistries, such as mercaptothreonine ligation (T205), diselenide-selenoester ligation (D358), and mutations of mercaptoamino acids into native residues via homogeneous radical desulfurization (A40, A77, A119, A157, A246, and A390). The successful completion of the synthesis has established a robust and scalable route to the native protein in multimilligram quantities and high purity. In broader terms, the presented strategy can be applied to the preparation of other shorter isoforms of Tau as well as to introduce all post-translational modifications that are characteristic of tauopathies such as AD.
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Affiliation(s)
- Wyatt C Powell
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Ruiheng Jing
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Maciej A Walczak
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
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7
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Ramirez J, Pancoe SX, Rhoades E, Petersson EJ. The Effects of Lipids on α-Synuclein Aggregation In Vitro. Biomolecules 2023; 13:1476. [PMID: 37892158 PMCID: PMC10604467 DOI: 10.3390/biom13101476] [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: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
The small neuronal protein α-synuclein (αS) is found in pre-synaptic terminals and plays a role in vesicle recycling and neurotransmission. Fibrillar aggregates of αS are the hallmark of Parkinson's disease and related neurodegenerative disorders. In both health and disease, interactions with lipids influence αS's structure and function, prompting much study of the effects of lipids on αS aggregation. A comprehensive collection (126 examples) of aggregation rate data for various αS/lipid combinations was presented, including combinations of lipid variations and mutations or post-translational modifications of αS. These data were interpreted in terms of lipid structure to identify general trends. These tabulated data serve as a resource for the community to help in the interpretation of aggregation experiments with lipids and to be potentially used as inputs for computational models of lipid effects on aggregation.
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Affiliation(s)
- Jennifer Ramirez
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA;
| | - Samantha X. Pancoe
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104, USA
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8
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Ramezani M, Wagenknecht-Wiesner A, Wang T, Holowka DA, Eliezer D, Baird BA. Alpha synuclein modulates mitochondrial Ca 2+ uptake from ER during cell stimulation and under stress conditions. NPJ Parkinsons Dis 2023; 9:137. [PMID: 37741841 PMCID: PMC10518018 DOI: 10.1038/s41531-023-00578-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/08/2023] [Indexed: 09/25/2023] Open
Abstract
Alpha synuclein (a-syn) is an intrinsically disordered protein prevalent in neurons, and aggregated forms are associated with synucleinopathies including Parkinson's disease (PD). Despite the biomedical importance and extensive studies, the physiological role of a-syn and its participation in etiology of PD remain uncertain. We showed previously in model RBL cells that a-syn colocalizes with mitochondrial membranes, depending on formation of N-terminal helices and increasing with mitochondrial stress1. We have now characterized this colocalization and functional correlates in RBL, HEK293, and N2a cells. We find that expression of a-syn enhances stimulated mitochondrial uptake of Ca2+ from the ER, depending on formation of its N-terminal helices but not on its disordered C-terminal tail. Our results are consistent with a-syn acting as a tether between mitochondria and ER, and we show increased contacts between these two organelles using structured illumination microscopy. We tested mitochondrial stress caused by toxins related to PD, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP/MPP+) and carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and found that a-syn prevents recovery of stimulated mitochondrial Ca2+ uptake. The C-terminal tail, and not N-terminal helices, is involved in this inhibitory activity, which is abrogated when phosphorylation site serine-129 is mutated (S129A). Correspondingly, we find that MPTP/MPP+ and CCCP stress is accompanied by both phosphorylation (pS129) and aggregation of a-syn. Overall, our results indicate that a-syn can participate as a tethering protein to modulate Ca2+ flux between ER and mitochondria, with potential physiological significance. A-syn can also prevent cellular recovery from toxin-induced mitochondrial dysfunction, which may represent a pathological role of a-syn in the etiology of PD.
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Affiliation(s)
- Meraj Ramezani
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Tong Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - David A Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
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Chaturvedi M, Raj R, Yadav SK, Srivastava T, Devi S, Dharmadana D, Valéry C, Sharma SK, Kumar D, Priya S. Implications of In Vitro Multi-Serine Phosphorylation of Alpha-Synuclein in Aggregation and Cytotoxicity. ACS Chem Neurosci 2023; 14:3103-3112. [PMID: 37562012 DOI: 10.1021/acschemneuro.3c00234] [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: 08/12/2023] Open
Abstract
Post-translational modifications guide the functional diversity and identity of proteins. Phosphorylation is one such post-translational modification that has been reported in pathological proteins related to various neurodegenerative disorders such as α-synuclein (α-syn) phosphorylation in Parkinson's disease and other synucleinopathies. In α-syn, the phosphorylation has mostly been observed at S129; however, the occurrence of other serine modifications at S9, S42, and S87 is partially explored. In pathogenic conditions, where α-syn is phosphorylated by complex kinase pathways, multi-site modifications may happen and alter the mechanism of α-syn aggregation. Here, using Polo-like kinase 2 and G-protein coupled receptor kinase 4, the in vitro phosphorylation of α-syn was performed, which revealed multi-serine phosphorylation. Mass spectrometry with customized proteolytic digestion showed prominent phosphorylation at S129 and modifications at S87 and S42 with PLK2 and S87 with GRK4. The phosphorylation at the identified serine residues was further validated with NMR and western blotting. Multi-serine phosphorylation aggravates the aggregation potential of monomeric α-syn, seeding capacity, and cytotoxicity in the SH-SY5Y cell line. This study proposes evidence for in vitro multi-site phosphorylation and its significance in α-syn aggregation, toxicity, and related pathogenesis.
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Affiliation(s)
- Minal Chaturvedi
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- School of Health and Biomedical Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Ritu Raj
- Centre of BioMedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Sanjeev Kumar Yadav
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tulika Srivastava
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shweta Devi
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Durga Dharmadana
- School of Health and Biomedical Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Céline Valéry
- School of Health and Biomedical Science, RMIT University, Bundoora, Victoria 3083, Australia
| | - Sandeep K Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Food, Drug & Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
| | - Dinesh Kumar
- Centre of BioMedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences Campus, Raebareli Road, Lucknow 226014, Uttar Pradesh, India
| | - Smriti Priya
- Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan 31, MG Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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10
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Motaln H, Rogelj B. The Role of c-Abl Tyrosine Kinase in Brain and Its Pathologies. Cells 2023; 12:2041. [PMID: 37626851 PMCID: PMC10453230 DOI: 10.3390/cells12162041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Differentiated status, low regenerative capacity and complex signaling make neuronal tissues highly susceptible to translating an imbalance in cell homeostasis into cell death. The high rate of neurodegenerative diseases in the elderly population confirms this. The multiple and divergent signaling cascades downstream of the various stress triggers challenge researchers to identify the central components of the stress-induced signaling pathways that cause neurodegeneration. Because of their critical role in cell homeostasis, kinases have emerged as one of the key regulators. Among kinases, non-receptor tyrosine kinase (Abelson kinase) c-Abl appears to be involved in both the normal development of neural tissue and the development of neurodegenerative pathologies when abnormally expressed or activated. However, exactly how c-Abl mediates the progression of neurodegeneration remains largely unexplored. Here, we summarize recent findings on the involvement of c-Abl in normal and abnormal processes in nervous tissue, focusing on neurons, astrocytes and microglial cells, with particular reference to molecular events at the interface between stress signaling, DNA damage, and metabolic regulation. Because inhibition of c-Abl has neuroprotective effects and can prevent neuronal death, we believe that an integrated view of c-Abl signaling in neurodegeneration could lead to significantly improved treatment of the disease.
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Affiliation(s)
- Helena Motaln
- Department of Biotechnology, Jozef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Boris Rogelj
- Department of Biotechnology, Jozef Stefan Institute, 1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia;
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11
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Uceda AB, Frau J, Vilanova B, Adrover M. Tyrosine Nitroxidation Does Not Affect the Ability of α-Synuclein to Bind Anionic Micelles, but It Diminishes Its Ability to Bind and Assemble Synaptic-like Vesicles. Antioxidants (Basel) 2023; 12:1310. [PMID: 37372040 DOI: 10.3390/antiox12061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Parkinson's disease (PD) is characterized by dopaminergic neuron degeneration and the accumulation of neuronal inclusions known as Lewy bodies, which are formed by aggregated and post-translationally modified α-synuclein (αS). Oxidative modifications such as the formation of 3-nitrotyrosine (3-NT) or di-tyrosine are found in αS deposits, and they could be promoted by the oxidative stress typical of PD brains. Many studies have tried to elucidate the molecular mechanism correlating nitroxidation, αS aggregation, and PD. However, it is unclear how nitroxidation affects the physiological function of αS. To clarify this matter, we synthetized an αS with its Tyr residues replaced by 3-NT. Its study revealed that Tyr nitroxidation had no effect on either the affinity of αS towards anionic micelles nor the overall structure of the micelle-bound αS, which retained its α-helical folding. Nevertheless, we observed that nitroxidation of Y39 lengthened the disordered stretch bridging the two consecutive α-helices. Conversely, the affinity of αS towards synaptic-like vesicles diminished as a result of Tyr nitroxidation. Additionally, we also proved that nitroxidation precluded αS from performing its physiological function as a catalyst of the clustering and the fusion of synaptic vesicles. Our findings represent a step forward towards the completion of the puzzle that must explain the molecular mechanism behind the link between αS-nitroxidation and PD.
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Affiliation(s)
- Ana Belén Uceda
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Health Research Institute of the Balearic Islands (IdISBa), E-07120 Palma de Mallorca, Spain
- Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
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12
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Brembati V, Faustini G, Longhena F, Bellucci A. Alpha synuclein post translational modifications: potential targets for Parkinson's disease therapy? Front Mol Neurosci 2023; 16:1197853. [PMID: 37305556 PMCID: PMC10248004 DOI: 10.3389/fnmol.2023.1197853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 06/13/2023] Open
Abstract
Parkinson's disease (PD) is the most common neurodegenerative disorder with motor symptoms. The neuropathological alterations characterizing the brain of patients with PD include the loss of dopaminergic neurons of the nigrostriatal system and the presence of Lewy bodies (LB), intraneuronal inclusions that are mainly composed of alpha-synuclein (α-Syn) fibrils. The accumulation of α-Syn in insoluble aggregates is a main neuropathological feature in PD and in other neurodegenerative diseases, including LB dementia (LBD) and multiple system atrophy (MSA), which are therefore defined as synucleinopathies. Compelling evidence supports that α-Syn post translational modifications (PTMs) such as phosphorylation, nitration, acetylation, O-GlcNAcylation, glycation, SUMOylation, ubiquitination and C-terminal cleavage, play important roles in the modulation α-Syn aggregation, solubility, turnover and membrane binding. In particular, PTMs can impact on α-Syn conformational state, thus supporting that their modulation can in turn affect α-Syn aggregation and its ability to seed further soluble α-Syn fibrillation. This review focuses on the importance of α-Syn PTMs in PD pathophysiology but also aims at highlighting their general relevance as possible biomarkers and, more importantly, as innovative therapeutic targets for synucleinopathies. In addition, we call attention to the multiple challenges that we still need to face to enable the development of novel therapeutic approaches modulating α-Syn PTMs.
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Affiliation(s)
| | | | | | - Arianna Bellucci
- Division of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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13
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Ramezani M, Wagenknecht-Wiesner A, Wang T, Holowka DA, Eliezer D, Baird BA. Alpha Synuclein Modulates Mitochondrial Ca 2+ Uptake from ER During Cell Stimulation and Under Stress Conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.23.537965. [PMID: 37163091 PMCID: PMC10168219 DOI: 10.1101/2023.04.23.537965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Alpha synuclein (a-syn) is an intrinsically disordered protein prevalent in neurons, and aggregated forms are associated with synucleinopathies including Parkinson' disease (PD). Despite the biomedical importance and extensive studies, the physiological role of a-syn and its participation in etiology of PD remain uncertain. We showed previously in model RBL cells that a-syn colocalizes with mitochondrial membranes, depending on formation of N-terminal helices and increasing with mitochondrial stress. 1 We have now characterized this colocalization and functional correlates in RBL, HEK293, and N2a cells. We find that expression of a-syn enhances stimulated mitochondrial uptake of Ca 2+ from the ER, depending on formation of its N-terminal helices but not on its disordered C-terminal tail. Our results are consistent with a-syn acting as a tether between mitochondria and ER, and we show increased contacts between these two organelles using structured illumination microscopy. We tested mitochondrial stress caused by toxins related to PD, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP/MPP+) and carbonyl cyanide m-chlorophenyl hydrazone (CCCP), and found that a-syn prevents recovery of stimulated mitochondrial Ca 2+ uptake. The C-terminal tail, and not N-terminal helices, is involved in this inhibitory activity, which is abrogated when phosphorylation site serine-129 is mutated (S129A). Correspondingly, we find that MPTP/MPP+ and CCCP stress is accompanied by both phosphorylation (pS129) and aggregation of a-syn. Overall, our results indicate that a-syn can participate as a tethering protein to modulate Ca 2+ flux between ER and mitochondria, with potential physiological significance. A-syn can also prevent cellular recovery from toxin-induced mitochondrial dysfunction, which may represent a pathological role of a-syn in the etiology of PD.
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Affiliation(s)
- Meraj Ramezani
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | | | - Tong Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - David A. Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065
| | - Barbara A. Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
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14
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Uceda AB, Frau J, Vilanova B, Adrover M. On the effect of methionine oxidation on the interplay between α-synuclein and synaptic-like vesicles. Int J Biol Macromol 2023; 229:92-104. [PMID: 36584779 DOI: 10.1016/j.ijbiomac.2022.12.262] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022]
Abstract
Human alpha-synuclein (αS) is an intrinsically disordered protein highly expressed in dopaminergic neurons. Its amyloid aggregates are the major component of Lewy bodies, which are considered a hallmark of Parkinson's disease (PD). αS has four different Met, which are particularly sensitive to oxidation, as most of them are found as Met sulfoxide (MetO) in the αS deposits. Consequently, researchers have invested mounting efforts trying to elucidate the molecular mechanisms underlying the links between oxidative stress, αS aggregation and PD. However, it has not been described yet the effect of Met oxidation on the physiological function of αS. Trying to shed light on this aspect, we have here studied a synthetic αS that displayed all its Met replaced by MetO moieties (αS-MetO). Our study has allowed to prove that MetO diminishes the affinity of αS towards anionic micelles (SDS), although the micelle-bound fraction of αS-MetO still adopts an α-helical folding resembling that of the lipid-bound αS. MetO also diminishes the affinity of αS towards synaptic-like vesicles, and its hindering effect is much more pronounced than that displayed on the αS-micelle affinity. Additionally, we have also demonstrated that MetO impairs the physiological function of αS as a catalyst of the clustering and the fusion of synaptic vesicles (SVs). Our findings provide a new understanding on how Met oxidation affects one of the most relevant biological functions attributed to αS that is to bind and cluster SVs along the neurotransmission.
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Affiliation(s)
- Ana Belén Uceda
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Departament de Química, Universitat de les Illes Balears, Ctra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain.
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15
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Zhang S, Zhu R, Pan B, Xu H, Olufemi MF, Gathagan RJ, Li Y, Zhang L, Zhang J, Xiang W, Kagan EM, Cao X, Yuan C, Kim SJ, Williams CK, Magaki S, Vinters HV, Lashuel HA, Garcia BA, James Petersson E, Trojanowski JQ, Lee VMY, Peng C. Post-translational modifications of soluble α-synuclein regulate the amplification of pathological α-synuclein. Nat Neurosci 2023; 26:213-225. [PMID: 36690898 PMCID: PMC10103650 DOI: 10.1038/s41593-022-01239-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 11/29/2022] [Indexed: 01/24/2023]
Abstract
Cell-to-cell transmission and subsequent amplification of pathological proteins promote neurodegenerative disease progression. Most research on this has focused on pathological protein seeds, but how their normal counterparts, which are converted to pathological forms during transmission, regulate transmission is less understood. Here we show in cultured cells that phosphorylation of soluble, nonpathological α-synuclein (α-Syn) at previously identified sites dramatically affects the amplification of pathological α-Syn, which underlies Parkinson's disease and other α-synucleinopathies, in a conformation- and phosphorylation site-specific manner. We performed LC-MS/MS analyses on soluble α-Syn purified from Parkinson's disease and other α-synucleinopathies, identifying many new α-Syn post-translational modifications (PTMs). In addition to phosphorylation, acetylation of soluble α-Syn also modified pathological α-Syn transmission in a site- and conformation-specific manner. Moreover, phosphorylation of soluble α-Syn could modulate the seeding properties of pathological α-Syn. Our study represents the first systematic analysis how of soluble α-Syn PTMs affect the spreading and amplification of pathological α-Syn, which may affect disease progression.
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Affiliation(s)
- Shujing Zhang
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Ruowei Zhu
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Buyan Pan
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Hong Xu
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Modupe F Olufemi
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald J Gathagan
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuanxi Li
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
- Institute for Cognitive Neurodynamics, East China University of Science and Technology, Shanghai, China
- School of Mathematics, East China University of Science and Technology, Shanghai, China
| | - Luyan Zhang
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Jasmine Zhang
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Wenxuan Xiang
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Eliot Masahiro Kagan
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | | | | | - Soo-Jung Kim
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher K Williams
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center and David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Shino Magaki
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, Ronald Reagan UCLA Medical Center and David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA
| | - Harry V Vinters
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, Department of Neurology, and Brain Research Institute, Ronald Reagan UCLA Medical Center and David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University St Louis, St Louis, MO, USA
| | - E James Petersson
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia M-Y Lee
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Chao Peng
- Department of Neurology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
- Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA.
- Mary S. Easton Center for Alzheimer's Research, University of California, Los Angeles, Los Angeles, CA, USA.
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16
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Pancoe SX, Wang YJ, Shimogawa M, Perez RM, Giannakoulias S, Petersson EJ. Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation. J Mol Biol 2022; 434:167859. [PMID: 36270580 PMCID: PMC9922159 DOI: 10.1016/j.jmb.2022.167859] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Fibrillar aggregates of the α-synuclein (αS) protein are the hallmark of Parkinson's Disease and related neurodegenerative disorders. Characterization of the effects of mutations and post-translational modifications (PTMs) on the αS aggregation rate can provide insight into the mechanism of fibril formation, which remains elusive in spite of intense study. A comprehensive collection (375 examples) of mutant and PTM aggregation rate data measured using the fluorescent probe thioflavin T is presented, as well as a summary of the effects of fluorescent labeling on αS aggregation (20 examples). A curated set of 131 single mutant de novo aggregation experiments are normalized to wild type controls and analyzed in terms of structural data for the monomer and fibrillar forms of αS. These tabulated data serve as a resource to the community to help in interpretation of aggregation experiments and to potentially be used as inputs for computational models of aggregation.
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Affiliation(s)
- Samantha X Pancoe
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Marie Shimogawa
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Ryann M Perez
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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17
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The Role of Membrane Affinity and Binding Modes in Alpha-Synuclein Regulation of Vesicle Release and Trafficking. Biomolecules 2022; 12:biom12121816. [PMID: 36551244 PMCID: PMC9775087 DOI: 10.3390/biom12121816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/02/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
Alpha-synuclein is a presynaptic protein linked to Parkinson's disease with a poorly characterized physiological role in regulating the synaptic vesicle cycle. Using RBL-2H3 cells as a model system, we earlier reported that wild-type alpha-synuclein can act as both an inhibitor and a potentiator of stimulated exocytosis in a concentration-dependent manner. The inhibitory function is constitutive and depends on membrane binding by the helix-2 region of the lipid-binding domain, while potentiation becomes apparent only at high concentrations. Using structural and functional characterization of conformationally selective mutants via a combination of spectroscopic and cellular assays, we show here that binding affinity for isolated vesicles similar in size to synaptic vesicles is a primary determinant of alpha-synuclein-mediated potentiation of vesicle release. Inhibition of release is sensitive to changes in the region linking the helix-1 and helix-2 regions of the N-terminal lipid-binding domain and may require some degree of coupling between these regions. Potentiation of release likely occurs as a result of alpha-synuclein interactions with undocked vesicles isolated away from the active zone in internal pools. Consistent with this, we observe that alpha-synuclein can disperse vesicles from in vitro clusters organized by condensates of the presynaptic protein synapsin-1.
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18
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Reimer L, Gram H, Jensen NM, Betzer C, Yang L, Jin L, Shi M, Boudeffa D, Fusco G, De Simone A, Kirik D, Lashuel HA, Zhang J, Jensen PH. Protein kinase R dependent phosphorylation of α-synuclein regulates its membrane binding and aggregation. PNAS NEXUS 2022; 1:pgac259. [PMID: 36712380 PMCID: PMC9802061 DOI: 10.1093/pnasnexus/pgac259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
Aggregated α-synuclein (α-syn) accumulates in the neuronal Lewy body (LB) inclusions in Parkinson's disease (PD) and LB dementia. Yet, under nonpathological conditions, monomeric α-syn is hypothesized to exist in an equilibrium between disordered cytosolic- and partially α-helical lipid-bound states: a feature presumably important in synaptic vesicle release machinery. The exact underlying role of α-syn in these processes, and the mechanisms regulating membrane-binding of α-syn remains poorly understood. Herein we demonstrate that Protein kinase R (PKR) can phosphorylate α-syn at several Ser/Thr residues located in the membrane-binding region that is essential for α-syn's vesicle-interactions. α-Syn phosphorylated by PKR or α-syn isolated from PKR overexpressing cells, exhibit decreased binding to lipid membranes. Phosphorylation of Thr64 and Thr72 appears as the major contributor to this effect, as the phosphomimetic Thr64Glu/Thr72Glu-α-syn mutant displays reduced overall attachment to brain vesicles due to a decrease in vesicle-affinity of the last two thirds of α-syn's membrane binding region. This allows enhancement of the "double-anchor" vesicle-binding mechanism that tethers two vesicles and thus promote the clustering of presynaptic vesicles in vitro. Furthermore, phosphomimetic Thr64Glu/Thr72Glu-α-syn inhibits α-syn oligomerization and completely abolishes nucleation, elongation, and seeding of α-syn fibrillation in vitro and in cells, and prevents trans-synaptic spreading of aggregated α-syn pathology in organotypic hippocampal slice cultures. Overall, our findings demonstrate that normal and abnormal functions of α-syn, like membrane-binding, synaptic vesicle clustering and aggregation can be regulated by phosphorylation, e.g., via PKR. Mechanisms that could potentially be modulated for the benefit of patients suffering from α-syn aggregate-related diseases.
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Affiliation(s)
| | - Hjalte Gram
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, 8000 Aarhus C, Denmark,Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Nanna Møller Jensen
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, 8000 Aarhus C, Denmark,Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Cristine Betzer
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, 8000 Aarhus C, Denmark,Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Li Yang
- Department of Pathology, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Lorrain Jin
- Department of Pathology, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Min Shi
- Department of Pathology, University of Washington School of Medicine, Seattle WA 98195, USA
| | - Driss Boudeffa
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind Institute, Station 19, 1015 Lausanne, Switzerland
| | - Giuliana Fusco
- Centre for Misfolding Diseases,Department of Chemistry, University of Cambridge, CB2 1EW, UK
| | | | - Deniz Kirik
- Brain Repair and Imaging in Neural Systems, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences Brain Mind Institute, Station 19, 1015 Lausanne, Switzerland
| | - Jing Zhang
- Department of Pathology, University of Washington School of Medicine, Seattle WA 98195, USA,Department of Pathology, Zhejiang University School of Medicine and the First Affiliated Hospital, 310003 Hangzhou, China
| | - Poul Henning Jensen
- Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, 8000 Aarhus C, Denmark,Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
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19
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Altay MF, Liu AKL, Holton JL, Parkkinen L, Lashuel HA. Prominent astrocytic alpha-synuclein pathology with unique post-translational modification signatures unveiled across Lewy body disorders. Acta Neuropathol Commun 2022; 10:163. [PMID: 36371251 PMCID: PMC9652889 DOI: 10.1186/s40478-022-01468-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/24/2022] [Indexed: 11/15/2022] Open
Abstract
Alpha-synuclein (aSyn) is a pre-synaptic monomeric protein that can form aggregates in neurons in Parkinson's disease (PD), Parkinson's disease with dementia (PDD) and dementia with Lewy bodies (DLB), and in oligodendrocytes in multiple system atrophy (MSA). Although aSyn in astrocytes has previously been described in PD, PDD and DLB, the biochemical properties and topographical distribution of astrocytic aSyn have not been studied in detail. Here, we present a systematic investigation of aSyn astrocytic pathology using an expanded antibody toolset covering the entire sequence and key post-translational modifications (PTMs) of aSyn in Lewy body disorders (LBDs) and in MSA. Astrocytic aSyn was detected in the limbic cortical regions of LBDs but were absent in main pathological regions of MSA. The astrocytic aSyn was revealed only with antibodies against the mid N-terminal and non-amyloid component (NAC) regions covering aSyn residues 34-99. The astroglial accumulations were negative to canonical aSyn aggregation markers, including p62, ubiquitin and aSyn pS129, but positive for phosphorylated and nitrated forms of aSyn at Tyrosine 39 (Y39), and not resistant to proteinase K. Our findings suggest that astrocytic aSyn accumulations represent a major part of aSyn pathology in LBDs and possess a distinct sequence and PTM signature that is characterized by both N- and C-terminal truncations and modifications at Y39. This is the first description that aSyn accumulations are made solely from N- and C-terminally cleaved aSyn species and the first report demonstrating that astrocytic aSyn is a mixture of Y39 phosphorylated and nitrated species. These observations underscore the importance of systematic characterization of aSyn accumulations in different cell types to capture the aSyn pathological diversity in the brain. Our findings combined with further studies on the role of astrocytic pathology in the progression of LBDs can pave the way towards identifying novel disease mechanisms and therapeutic targets.
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Affiliation(s)
- Melek Firat Altay
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Alan King Lun Liu
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, West Wing, Level 6, Oxford, OX3 9DU, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, University College London Queen Square Institute of Neurology, London, England
| | - Laura Parkkinen
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK.
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, West Wing, Level 6, Oxford, OX3 9DU, UK.
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland.
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20
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Opportunities and challenges of alpha-synuclein as a potential biomarker for Parkinson's disease and other synucleinopathies. NPJ Parkinsons Dis 2022; 8:93. [PMID: 35869066 PMCID: PMC9307631 DOI: 10.1038/s41531-022-00357-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/24/2022] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s disease (PD), the second most common progressive neurodegenerative disease, develops and progresses for 10–15 years before the clinical diagnostic symptoms of the disease are manifested. Furthermore, several aspects of PD pathology overlap with other neurodegenerative diseases (NDDs) linked to alpha-synuclein (aSyn) aggregation, also called synucleinopathies. Therefore, there is an urgent need to discover and validate early diagnostic and prognostic markers that reflect disease pathophysiology, progression, severity, and potential differences in disease mechanisms between PD and other NDDs. The close association between aSyn and the development of pathology in synucleinopathies, along with the identification of aSyn species in biological fluids, has led to increasing interest in aSyn species as potential biomarkers for early diagnosis of PD and differentiate it from other synucleinopathies. In this review, we (1) provide an overview of the progress toward mapping the distribution of aSyn species in the brain, peripheral tissues, and biological fluids; (2) present comparative and critical analysis of previous studies that measured total aSyn as well as other species such as modified and aggregated forms of aSyn in different biological fluids; and (3) highlight conceptual and technical gaps and challenges that could hinder the development and validation of reliable aSyn biomarkers; and (4) outline a series of recommendations to address these challenges. Finally, we propose a combined biomarker approach based on integrating biochemical, aggregation and structure features of aSyn, in addition to other biomarkers of neurodegeneration. We believe that capturing the diversity of aSyn species is essential to develop robust assays and diagnostics for early detection, patient stratification, monitoring of disease progression, and differentiation between synucleinopathies. This could transform clinical trial design and implementation, accelerate the development of new therapies, and improve clinical decisions and treatment strategies.
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21
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Petricca L, Chiki N, Hanna-El-Daher L, Aeschbach L, Burai R, Stoops E, Fares MB, Lashuel HA. Comparative Analysis of Total Alpha-Synuclein (αSYN) Immunoassays Reveals That They Do Not Capture the Diversity of Modified αSYN Proteoforms. JOURNAL OF PARKINSON'S DISEASE 2022; 12:1449-1462. [PMID: 35527570 PMCID: PMC9398082 DOI: 10.3233/jpd-223285] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background: The development of therapeutics for Parkinson’s disease (PD) requires the establishment of biomarker assays to enable stratifying patients, monitoring disease progression, and assessing target engagement. Attempts to develop diagnostic assays based on detecting levels of the α-synuclein (αSYN) protein, a central player in the pathogenesis of PD, have yielded inconsistent results. Objective: To determine whether the three commercial kits that have been extensively used for total αSYN quantification in human biological fluids (from Euroimmun, MSD, and Biolegend) are capable of capturing the diversity and complexity of relevant αSYN proteoforms. Methods: We investigated and compared the ability of the different assays to detect the diversity of αSYN proteoforms using a library of αSYN proteins that comprise the majority of disease-relevant αSYN variants and post-translational modifications (PTMs). Results: Our findings showed that none of the three tested immunoassays accurately capture the totality of relevant αSYN species, and that these assays are unable to recognize most disease-associated C-terminally truncated variants of αSYN. Moreover, several N-terminal truncations and phosphorylation/nitration PTMs differentially modify the level of αSYN detection and recovery by different immunoassays, and a CSF matrix effect was observed for most of the αSYN proteoforms analyzed by the three immunoassays. Conclusion: Our results show that the tested immunoassays do not capture the totality of the relevant αSYN species and therefore may not be appropriate tools to provide an accurate measure of total αSYN levels in samples containing modified forms of the protein. This highlights the need for next generation αSYN immunoassays that capture the diversity of αSYN proteoforms.
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Affiliation(s)
| | - Nour Chiki
- ND Biosciences SA, Epalinges, Switzerland
| | - Layane Hanna-El-Daher
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lorène Aeschbach
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ritwik Burai
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erik Stoops
- ADx NeuroSciences NV, Technologiepark 94 - Bio Incubator, Gent, Belgium
| | | | - Hilal A Lashuel
- ND Biosciences SA, Epalinges, Switzerland.,Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute,Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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22
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Buratti FA, Boeffinger N, Garro HA, Flores JS, Hita FJ, Gonçalves PDC, Copello FDR, Lizarraga L, Rossetti G, Carloni P, Zweckstetter M, Outeiro TF, Eimer S, Griesinger C, Fernández CO. Aromaticity at position 39 in α-synuclein: A modulator of amyloid fibril assembly and membrane-bound conformations. Protein Sci 2022; 31:e4360. [PMID: 35762717 PMCID: PMC9235065 DOI: 10.1002/pro.4360] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 12/20/2022]
Abstract
Recent studies revealed that molecular events related with the physiology and pathology of αS might be regulated by specific sequence motifs in the primary sequence of αS. The importance of individual residues in these motifs remains an important open avenue of investigation. In this work, we have addressed the structural details related to the amyloid fibril assembly and lipid-binding features of αS through the design of site-directed mutants at position 39 of the protein and their study by in vitro and in vivo assays. We demonstrated that aromaticity at position 39 of αS primary sequence influences strongly the aggregation properties and the membrane-bound conformations of the protein, molecular features that might have important repercussions for the function and dysfunction of αS. Considering that aggregation and membrane damage is an important driver of cellular toxicity in amyloid diseases, future work is needed to link our findings with studies based on toxicity and neuronal cell death. BRIEF STATEMENT OUTLINING SIGNIFICANCE: Modulation by distinct sequential motifs and specific residues of αS on its physiological and pathological states is an active area of research. Here, we demonstrated that aromaticity at position 39 of αS modulates the membrane-bound conformations of the protein, whereas removal of aromatic functionality at position 39 reduces strongly the amyloid assembly in vitro and in vivo. Our study provides new evidence for the modulation of molecular events related with the physiology and pathology of αS.
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Affiliation(s)
- Fiamma A. Buratti
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR‐MPINAT)Partner Laboratory of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de RosarioRosarioArgentina
| | - Nicola Boeffinger
- Department of NMR‐based Structural BiologyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Department of Structural Cell Biology, Institute for Cell Biology and NeuroscienceGoethe University FrankfurtFrankfurtGermany
| | - Hugo A. Garro
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR‐MPINAT)Partner Laboratory of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de RosarioRosarioArgentina
- Area de Química OrgánicaUNSL‐INTEQUI/CONICETSan LuisArgentina
| | - Jesica S. Flores
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR‐MPINAT)Partner Laboratory of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de RosarioRosarioArgentina
| | - Francisco J. Hita
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR‐MPINAT)Partner Laboratory of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de RosarioRosarioArgentina
| | - Phelippe do Carmo Gonçalves
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR‐MPINAT)Partner Laboratory of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de RosarioRosarioArgentina
| | | | - Leonardo Lizarraga
- Centro de Investigaciones en Bionanociencias (CIBION‐CONICET)Buenos AiresArgentina
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM‐9) and Institute for Advanced Simulations (IAS‐5)JülichGermany
- Department of NeurologyUniversity Hospital Aachen, RWTH Aachen UniversityAachenGermany
- Jülich Supercomputing Center (JSC)JülichGermany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Neuroscience and Medicine (INM‐9) and Institute for Advanced Simulations (IAS‐5)JülichGermany
- Faculty of Mathematics, Computer Science and Natural SciencesRWTH AachenAachenGermany
- Institute for Neuroscience and Medicine (INM‐11) Forschungszentrum JülichJülichGermany
| | - Markus Zweckstetter
- Department of NMR‐based Structural BiologyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
- German Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Tiago F. Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of NeurodegenerationUniversity Medical Center GöttingenGöttingenGermany
- Translational and Clinical Research InstituteNewcastle UniversityNewcastleUK
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)GöttingenGermany
| | - Stefan Eimer
- Department of Structural Cell Biology, Institute for Cell Biology and NeuroscienceGoethe University FrankfurtFrankfurtGermany
| | - Christian Griesinger
- Department of NMR‐based Structural BiologyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Claudio O. Fernández
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR‐MPINAT)Partner Laboratory of the Max Planck Institute for Multidisciplinary Sciences (MPINAT, MPG). Centro de Estudios Interdisciplinarios, Universidad Nacional de RosarioRosarioArgentina
- Department of NMR‐based Structural BiologyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
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23
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Bilbrough T, Piemontese E, Seitz O. Dissecting the role of protein phosphorylation: a chemical biology toolbox. Chem Soc Rev 2022; 51:5691-5730. [PMID: 35726784 DOI: 10.1039/d1cs00991e] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is a crucial regulator of protein and cellular function, yet, despite identifying an enormous number of phosphorylation sites, the role of most is still unclear. Each phosphoform, the particular combination of phosphorylations, of a protein has distinct and diverse biological consequences. Aberrant phosphorylation is implicated in the development of many diseases. To investigate their function, access to defined protein phosphoforms is essential. Materials obtained from cells often are complex mixtures. Recombinant methods can provide access to defined phosphoforms if site-specifically acting kinases are known, but the methods fail to provide homogenous material when several amino acid side chains compete for phosphorylation. Chemical and chemoenzymatic synthesis has provided an invaluable toolbox to enable access to previously unreachable phosphoforms of proteins. In this review, we selected important tools that enable access to homogeneously phosphorylated protein and discuss examples that demonstrate how they can be applied. Firstly, we discuss the synthesis of phosphopeptides and proteins through chemical and enzymatic means and their advantages and limitations. Secondly, we showcase illustrative examples that applied these tools to answer biological questions pertaining to proteins involved in signal transduction, control of transcription, neurodegenerative diseases and aggregation, apoptosis and autophagy, and transmembrane proteins. We discuss the opportunities and challenges in the field.
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Affiliation(s)
- Tim Bilbrough
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Emanuele Piemontese
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany.
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24
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Uceda AB, Frau J, Vilanova B, Adrover M. Glycation of α-synuclein hampers its binding to synaptic-like vesicles and its driving effect on their fusion. Cell Mol Life Sci 2022; 79:342. [PMID: 35662377 PMCID: PMC9167179 DOI: 10.1007/s00018-022-04373-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
Parkinson's disease (PD) is one of the most prevalent neurodegenerative disorders affecting the worldwide population. One of its hallmarks is the intraneuronal accumulation of insoluble Lewy bodies (LBs), which cause the death of dopaminergic neurons. α-Synuclein (αS) is the main component of these LBs and in them, it commonly contains non-enzymatic post-translational modifications, such as those resulting from its reaction with reactive carbonyl species arising as side products of the intraneuronal glycolysis (mainly methylglyoxal). Consequently, lysines of the αS found in LBs of diabetic individuals are usually carboxyethylated. A precise comprehension of the effect of Nε-(carboxyethyl)lysine (CEL) on the aggregation of αS and on its physiological function becomes crucial to fully understand the molecular mechanisms underlying the development of diabetes-induced PD. Consequently, we have here used a synthetic αS where all its Lys have been replaced by CEL moieties (αS-CEL), and we have studied how these modifications could impact on the neurotransmission mechanism. This study allows us to describe how the non-enzymatic glycosylation (glycation) affects the function of a protein like αS, involved in the pathogenesis of PD. CEL decreases the ability of αS to bind micelles, although the micelle-bound fraction of αS-CEL still displays an α-helical fold resembling that of the lipid-bound αS. However, CEL completely abolishes the affinity of αS towards synaptic-like vesicles and, consequently, it hampers its physiological function as a catalyst of the clustering and the fusion of the synaptic vesicles.
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Affiliation(s)
- Ana Belén Uceda
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Juan Frau
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Bartolomé Vilanova
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain
| | - Miquel Adrover
- Departament de Química, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Institut de Recerca en Ciències de la Salut (IdISBa), Universitat de les Illes Balears, Ed. Mateu Orfila i Rotger, Ctra. Valldemossa km 7.5, 07122, Palma, Spain.
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25
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Calabrese G, Molzahn C, Mayor T. Protein interaction networks in neurodegenerative diseases: from physiological function to aggregation. J Biol Chem 2022; 298:102062. [PMID: 35623389 PMCID: PMC9234719 DOI: 10.1016/j.jbc.2022.102062] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/26/2022] [Accepted: 05/18/2022] [Indexed: 11/25/2022] Open
Abstract
The accumulation of protein inclusions is linked to many neurodegenerative diseases that typically develop in older individuals, due to a combination of genetic and environmental factors. In rare familial neurodegenerative disorders, genes encoding for aggregation-prone proteins are often mutated. While the underlying mechanism leading to these diseases still remains to be fully elucidated, efforts in the past 20 years revealed a vast network of protein–protein interactions that play a major role in regulating the aggregation of key proteins associated with neurodegeneration. Misfolded proteins that can oligomerize and form insoluble aggregates associate with molecular chaperones and other elements of the proteolytic machineries that are the frontline workers attempting to protect the cells by promoting clearance and preventing aggregation. Proteins that are normally bound to aggregation-prone proteins can become sequestered and mislocalized in protein inclusions, leading to their loss of function. In contrast, mutations, posttranslational modifications, or misfolding of aggregation-prone proteins can lead to gain of function by inducing novel or altered protein interactions, which in turn can impact numerous essential cellular processes and organelles, such as vesicle trafficking and the mitochondria. This review examines our current knowledge of protein–protein interactions involving several key aggregation-prone proteins that are associated with Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, or amyotrophic lateral sclerosis. We aim to provide an overview of the protein interaction networks that play a central role in driving or mitigating inclusion formation, while highlighting some of the key proteomic studies that helped to uncover the extent of these networks.
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Affiliation(s)
- Gaetano Calabrese
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada.
| | - Cristen Molzahn
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada
| | - Thibault Mayor
- Michael Smith Laboratories, University of British Columbia, V6T 1Z4 Vancouver BC, Canada.
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26
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Landrieu I, Dupré E, Sinnaeve D, El Hajjar L, Smet-Nocca C. Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools. Front Chem 2022; 10:886382. [PMID: 35646824 PMCID: PMC9133342 DOI: 10.3389/fchem.2022.886382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.
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Affiliation(s)
- Isabelle Landrieu
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Elian Dupré
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Davy Sinnaeve
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Léa El Hajjar
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
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27
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Antunes ASLM. Post-translational Modifications in Parkinson’s Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:85-94. [DOI: 10.1007/978-3-031-05460-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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28
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Acosta DM, Mancinelli C, Bracken C, Eliezer D. Post-translational modifications within tau paired helical filament nucleating motifs perturb microtubule interactions and oligomer formation. J Biol Chem 2021; 298:101442. [PMID: 34838590 PMCID: PMC8741514 DOI: 10.1016/j.jbc.2021.101442] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 10/25/2022] Open
Abstract
Post-translationally modified tau is the primary component of tau neurofibrillary tangles, a pathological hallmark of Alzheimer's disease and other tauopathies. Post-translational modifications within the tau microtubule binding domain (MBD), which encompasses two hexapeptide motifs that act as critical nucleating regions for tau aggregation, can potentially modulate tau aggregation as well as interactions with microtubules (MTs) and membranes. Here we characterize the effects of a recently discovered tau PTM, lysine succinylation, on tau-tubulin interactions, and compare these to the effects of two previously reported MBD modifications, lysine acetylation and tyrosine phosphorylation. As generation of site-specific PTMs in proteins is challenging, we used short synthetic peptides to quantify the effects on tubulin binding of three site-specific PTMs located within the PHF6* (residues 275-280) and PHF6 (residues 306-311) hexapeptide motifs: K280 acetylation, Y310 phosphorylation and K311 succinylation. We compared these effects to those observed for MBD PTM-mimetic point mutations K280Q, Y310E and K311E. Finally, we evaluated the effects of these PTM-mimetic mutations on MBD membrane binding and membrane-induced fibril and oligomer formation. We found that all three PTMs perturb tau MT binding, with Y310 phosphorylation exerting the strongest effect. PTM mimetic mutations partially recapitulated the effects of the PTMs on MT binding and also disrupted tau membrane binding and membrane induced oligomer and fibril formation. These results imply that these PTMs, including the novel and AD-specific succinylation of tau K311, may influence both the physiological and pathological interactions of tau and thus represent targets for therapeutic intervention.
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Affiliation(s)
- Diana M Acosta
- Feil Family Brain and Mind Research Institute, Department of Biochemistry and Program in Structural Biology, Weill Cornell Medicine, New York, NY 10065
| | - Chiara Mancinelli
- Department of Biochemistry and Program in Structural Biology, Weill Cornell Medicine, New York, NY 10065
| | - Clay Bracken
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - David Eliezer
- Feil Family Brain and Mind Research Institute, Department of Biochemistry and Program in Structural Biology, Weill Cornell Medicine, New York, NY 10065.
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29
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Srinivasan E, Chandrasekhar G, Chandrasekar P, Anbarasu K, Vickram AS, Karunakaran R, Rajasekaran R, Srikumar PS. Alpha-Synuclein Aggregation in Parkinson's Disease. Front Med (Lausanne) 2021; 8:736978. [PMID: 34733860 PMCID: PMC8558257 DOI: 10.3389/fmed.2021.736978] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Parkinson's disease (PD), a neurodegenerative disorder characterized by distinct aging-independent loss of dopaminergic neurons in substantia nigra pars compacta (SNpc) region urging toward neuronal loss. Over the decade, various key findings from clinical perspective to molecular pathogenesis have aided in understanding the genetics with assorted genes related with PD. Subsequently, several pathways have been incriminated in the pathogenesis of PD, involving mitochondrial dysfunction, protein aggregation, and misfolding. On the other hand, the sporadic form of PD cases is found with no genetic linkage, which still remain an unanswered question? The exertion in ascertaining vulnerability factors in PD considering the genetic factors are to be further dissevered in the forthcoming decades with advancement in research studies. One of the major proponents behind the prognosis of PD is the pathogenic transmutation of aberrant alpha-synuclein protein into amyloid fibrillar structures, which actuates neurodegeneration. Alpha-synuclein, transcribed by SNCA gene is a neuroprotein found predominantly in brain. It is implicated in the modulation of synaptic vesicle transport and eventual release of neurotransmitters. Due to genetic mutations and other elusive factors, the alpha-synuclein misfolds into its amyloid form. Therefore, this review aims in briefing the molecular understanding of the alpha-synuclein associated with PD.
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Affiliation(s)
- E Srinivasan
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India.,Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, India
| | - G Chandrasekhar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - P Chandrasekar
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - K Anbarasu
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, India
| | - A S Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, India
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Bedong, Malaysia
| | - R Rajasekaran
- Bioinformatics Lab, Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, India
| | - P S Srikumar
- Unit of Psychiatry, Faculty of Medicine, AIMST University, Bedong, Malaysia
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30
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Sarchione A, Marchand A, Taymans JM, Chartier-Harlin MC. Alpha-Synuclein and Lipids: The Elephant in the Room? Cells 2021; 10:2452. [PMID: 34572099 PMCID: PMC8467310 DOI: 10.3390/cells10092452] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/17/2022] Open
Abstract
Since the initial identification of alpha-synuclein (α-syn) at the synapse, numerous studies demonstrated that α-syn is a key player in the etiology of Parkinson's disease (PD) and other synucleinopathies. Recent advances underline interactions between α-syn and lipids that also participate in α-syn misfolding and aggregation. In addition, increasing evidence demonstrates that α-syn plays a major role in different steps of synaptic exocytosis. Thus, we reviewed literature showing (1) the interplay among α-syn, lipids, and lipid membranes; (2) advances of α-syn synaptic functions in exocytosis. These data underscore a fundamental role of α-syn/lipid interplay that also contributes to synaptic defects in PD. The importance of lipids in PD is further highlighted by data showing the impact of α-syn on lipid metabolism, modulation of α-syn levels by lipids, as well as the identification of genetic determinants involved in lipid homeostasis associated with α-syn pathologies. While questions still remain, these recent developments open the way to new therapeutic strategies for PD and related disorders including some based on modulating synaptic functions.
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Affiliation(s)
| | | | | | - Marie-Christine Chartier-Harlin
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172—LilNCog—Lille Neuroscience and Cognition, F-59000 Lille, France; (A.S.); (A.M.); (J.-M.T.)
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31
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Oliveira LMA, Gasser T, Edwards R, Zweckstetter M, Melki R, Stefanis L, Lashuel HA, Sulzer D, Vekrellis K, Halliday GM, Tomlinson JJ, Schlossmacher M, Jensen PH, Schulze-Hentrich J, Riess O, Hirst WD, El-Agnaf O, Mollenhauer B, Lansbury P, Outeiro TF. Alpha-synuclein research: defining strategic moves in the battle against Parkinson's disease. NPJ Parkinsons Dis 2021; 7:65. [PMID: 34312398 PMCID: PMC8313662 DOI: 10.1038/s41531-021-00203-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
With the advent of the genetic era in Parkinson's disease (PD) research in 1997, α-synuclein was identified as an important player in a complex neurodegenerative disease that affects >10 million people worldwide. PD has been estimated to have an economic impact of $51.9 billion in the US alone. Since the initial association with PD, hundreds of researchers have contributed to elucidating the functions of α-synuclein in normal and pathological states, and these remain critical areas for continued research. With this position paper the authors strive to achieve two goals: first, to succinctly summarize the critical features that define α-synuclein's varied roles, as they are known today; and second, to identify the most pressing knowledge gaps and delineate a multipronged strategy for future research with the goal of enabling therapies to stop or slow disease progression in PD.
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Affiliation(s)
- Luis M A Oliveira
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY, USA.
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Robert Edwards
- Departments of Neurology and Physiology, UCSF School of Medicine, San Francisco, CA, USA
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ronald Melki
- Institut François Jacob, MIRCen, CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Leonidas Stefanis
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- First Department of Neurology, Medical School of the National and Kapodistrian University of Athens, Athens, Greece
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Faculty of Life Sciences, EPFL, Lausanne, Switzerland
| | - David Sulzer
- Department of Psychiatry, Neurology, Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY, USA
| | - Kostas Vekrellis
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Glenda M Halliday
- University of Sydney, Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, Sydney, NSW, Australia
| | - Julianna J Tomlinson
- Neuroscience Program, The Ottawa Hospital, Ottawa, ON, Canada
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
| | - Michael Schlossmacher
- Neuroscience Program, The Ottawa Hospital, Ottawa, ON, Canada
- University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
- Division of Neurology, The Ottawa Hospital, Ottawa, ON, Canada
| | - Poul Henning Jensen
- Aarhus University, Department of Biomedicine & DANDRITE, Danish Research Institute of Translational Neuroscience, Aarhus, Denmark
| | - Julia Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Warren D Hirst
- Neurodegenerative Diseases Research Unit, Biogen, Cambridge, MA, USA
| | - Omar El-Agnaf
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Brit Mollenhauer
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Paracelsus-Elena-Klinik, Kassel, Germany
| | | | - Tiago F Outeiro
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
- Max Planck Institute for Experimental Medicine, Göttingen, Germany.
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
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32
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Bell R, Vendruscolo M. Modulation of the Interactions Between α-Synuclein and Lipid Membranes by Post-translational Modifications. Front Neurol 2021; 12:661117. [PMID: 34335440 PMCID: PMC8319954 DOI: 10.3389/fneur.2021.661117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease is characterised by the presence in brain tissue of aberrant inclusions known as Lewy bodies and Lewy neurites, which are deposits composed by α-synuclein and a variety of other cellular components, including in particular lipid membranes. The dysregulation of the balance between lipid homeostasis and α-synuclein homeostasis is therefore likely to be closely involved in the onset and progression of Parkinson's disease and related synucleinopathies. As our understanding of this balance is increasing, we describe recent advances in the characterisation of the role of post-translational modifications in modulating the interactions of α-synuclein with lipid membranes. We then discuss the impact of these advances on the development of novel diagnostic and therapeutic tools for synucleinopathies.
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Affiliation(s)
| | - Michele Vendruscolo
- Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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33
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Moon SP, Balana AT, Pratt MR. Consequences of post-translational modifications on amyloid proteins as revealed by protein semisynthesis. Curr Opin Chem Biol 2021; 64:76-89. [PMID: 34175787 DOI: 10.1016/j.cbpa.2021.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/21/2021] [Accepted: 05/09/2021] [Indexed: 12/17/2022]
Abstract
Alterations to the global levels of certain types of post-translational modifications (PTMs) are commonly observed in neurodegenerative diseases. The net influence of these PTM changes to the progression of these diseases can be deduced from cellular and animal studies. However, at the molecular level, how one PTM influences a given protein is not uniform and cannot be easily generalized from systemic observations, thus requiring protein-specific interrogations. Given that protein aggregation is a shared pathological hallmark in neurodegeneration, it is important to understand how these PTMs affect the behavior of amyloid-forming proteins. For this purpose, protein semisynthesis techniques, largely via native chemical and expressed protein ligation, have been widely used. These approaches have thus far led to our increased understanding of the site-specific consequences of certain PTMs to amyloidogenic proteins' endogenous function, their propensity for aggregation, and the structural variations these PTMs induce toward the aggregates formed.
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Affiliation(s)
- Stuart P Moon
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Aaron T Balana
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Matthew R Pratt
- Departments of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA; Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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34
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Pan B, Park JH, Ramlall T, Eliezer D, Rhoades E, Petersson EJ. Chemoenzymatic Semi-synthesis Enables Efficient Production of Isotopically Labeled α-Synuclein with Site-Specific Tyrosine Phosphorylation. Chembiochem 2021; 22:1440-1447. [PMID: 33274519 PMCID: PMC8185324 DOI: 10.1002/cbic.202000742] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/02/2020] [Indexed: 11/12/2022]
Abstract
Post-translational modifications (PTMs) can affect the normal function and pathology of α-synuclein (αS), an amyloid-fibril-forming protein linked to Parkinson's disease. Phosphorylation of αS Tyr39 has recently been found to display a dose-dependent effect on fibril formation kinetics and to alter the morphology of the fibrils. Existing methods to access site-specifically phosphorylated αS for biochemical studies include total or semi-synthesis by native chemical ligation (NCL) as well as chemoenzymatic methods to phosphorylate peptides, followed by NCL. Here, we investigated a streamlined method to produce large quantities of phosphorylated αS by co-expressing a kinase with a protein fragment in Escherichia coli. We also introduced the use of methyl thioglycolate (MTG) to enable one-pot NCL and desulfurization. We compare our optimized methods to previous reports and show that we can achieve the highest yields of site-specifically phosphorylated protein through chemoenzymatic methods using MTG, and that our strategy is uniquely well suited to producing 15 N-labeled, phosphorylated protein for NMR studies.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
| | - Joo Hyung Park
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
| | - Trudy Ramlall
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue; New York, NY, 10065
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue; New York, NY, 10065
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street; Philadelphia, Pennsylvania 19104-6323, USA
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35
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Braun T, Stehle J, Kacprzak S, Carl P, Höfer P, Subramaniam V, Drescher M. Intracellular Protein-Lipid Interactions Studied by Rapid-Scan Electron Paramagnetic Resonance Spectroscopy. J Phys Chem Lett 2021; 12:2471-2475. [PMID: 33663214 PMCID: PMC7957861 DOI: 10.1021/acs.jpclett.0c03583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Protein-membrane interactions play key roles in essential cellular processes; studying these interactions in the cell is a challenging task of modern biophysical chemistry. A prominent example is the interaction of human α-synuclein (αS) with negatively charged membranes. It has been well-studied in vitro, but in spite of the huge amount of lipid membranes in the crowded environment of biological cells, to date, no interactions have been detected in cells. Here, we use rapid-scan (RS) electron paramagnetic resonance (EPR) spectroscopy to study αS interactions with negatively charged vesicles in vitro and upon transfection of the protein and lipid vesicles into model cells, i.e., oocytes of Xenopus laevis. We show that protein-vesicle interactions are reflected in RS spectra in vitro and in cells, which enables time-resolved monitoring of protein-membrane interaction upon transfection into cells. Our data suggest binding of a small fraction of αS to endogenous membranes.
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Affiliation(s)
- Theresa
S. Braun
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Juliane Stehle
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sylwia Kacprzak
- Bruker BioSpin
GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Patrick Carl
- Bruker BioSpin
GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Peter Höfer
- Bruker BioSpin
GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Vinod Subramaniam
- Vrije
Universiteit Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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36
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Li D, Liu C. Hierarchical chemical determination of amyloid polymorphs in neurodegenerative disease. Nat Chem Biol 2021; 17:237-245. [PMID: 33432239 DOI: 10.1038/s41589-020-00708-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 11/10/2020] [Indexed: 01/28/2023]
Abstract
Amyloid aggregation, which disrupts protein homeostasis, is a common pathological event occurring in human neurodegenerative diseases (NDs). Numerous evidences have shown that the structural diversity, so-called polymorphism, is decisive to the amyloid pathology and is closely associated with the onset, progression, and phenotype of ND. But how could one protein form so many stable structures? Recently, atomic structural evidence has been rapidly mounting to depict the involvement of chemical modifications in the amyloid fibril formation. In this Perspective, we aim to present a hierarchical regulation of chemical modifications including covalent post-translational modifications (PTMs) and noncovalent cofactor binding in governing the polymorphic amyloid formation, based mainly on the latest α-synuclein and Tau fibril structures. We hope to emphasize the determinant role of chemical modifications in amyloid assembly and pathology and to evoke chemical biological approaches to lead the fundamental and therapeutic research on protein amyloid state and the associated NDs.
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Affiliation(s)
- Dan Li
- Bio-X-Renji Hospital Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
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37
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 386] [Impact Index Per Article: 128.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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38
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The docking of synaptic vesicles on the presynaptic membrane induced by α-synuclein is modulated by lipid composition. Nat Commun 2021; 12:927. [PMID: 33568632 PMCID: PMC7876145 DOI: 10.1038/s41467-021-21027-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
α-Synuclein (αS) is a presynaptic disordered protein whose aberrant aggregation is associated with Parkinson’s disease. The functional role of αS is still debated, although it has been involved in the regulation of neurotransmitter release via the interaction with synaptic vesicles (SVs). We report here a detailed characterisation of the conformational properties of αS bound to the inner and outer leaflets of the presynaptic plasma membrane (PM), using small unilamellar vesicles. Our results suggest that αS preferentially binds the inner PM leaflet. On the basis of these studies we characterise in vitro a mechanism by which αS stabilises, in a concentration-dependent manner, the docking of SVs on the PM by establishing a dynamic link between the two membranes. The study then provides evidence that changes in the lipid composition of the PM, typically associated with neurodegenerative diseases, alter the modes of binding of αS, specifically in a segment of the sequence overlapping with the non-amyloid component region. Taken together, these results reveal how lipid composition modulates the interaction of αS with the PM and underlie its functional and pathological behaviours in vitro. α-Synuclein is a presynaptic protein whose aberrant aggregation is associated with Parkinson’s disease. Here, the authors show how αSynuclein-induced docking of synaptic vesicles is modulated by the lipid composition changes typically observed in neurodegeneration using an in vitro system.
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39
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Pan B, Kamo N, Shimogawa M, Huang Y, Kashina A, Rhoades E, Petersson EJ. Effects of Glutamate Arginylation on α-Synuclein: Studying an Unusual Post-Translational Modification through Semisynthesis. J Am Chem Soc 2020; 142:21786-21798. [PMID: 33337869 DOI: 10.1021/jacs.0c10054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A variety of post-translational modifications (PTMs) are believed to regulate the behavior and function of α-synuclein (αS), an intrinsically disordered protein that mediates synaptic vesicle trafficking. Fibrils of αS are implicated in neurodegenerative disorders such as Parkinson's disease. In this study, we used chemical synthesis and biophysical techniques to characterize the neuroprotective effects of glutamate arginylation, a hitherto little characterized PTM in αS. We developed semisynthetic routes combining peptide synthesis, unnatural amino acid mutagenesis, and native chemical ligation (NCL) to site-specifically introduce the PTM of interest along with fluorescent probes into αS. We synthesized the arginylated glutamate as a protected amino acid, as well as a novel ligation handle for NCL, in order to generate full-length αS modified at various individual sites or a combination of sites. We assayed the lipid-vesicle binding affinities of arginylated αS using fluorescence correlation spectroscopy (FCS) and found that arginylated αS has the same vesicle affinity compared to control protein, suggesting that this PTM does not alter the native function of αS. On the other hand, we studied the aggregation kinetics of modified αS and found that arginylation at E83, but not E46, slows aggregation and decreases the percentage incorporation of monomer into fibrils in a dose-dependent manner. Arginylation at both sites also resulted in deceleration of fibril formation. Our study represents the first synthetic strategy for incorporating glutamate arginylation into proteins and provides insight into the neuroprotective effect of this unusual PTM.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Naoki Kamo
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States.,Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Marie Shimogawa
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Yun Huang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, Pennsylvania 19104, United States
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
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40
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Aspholm EE, Matečko-Burmann I, Burmann BM. Keeping α-Synuclein at Bay: A More Active Role of Molecular Chaperones in Preventing Mitochondrial Interactions and Transition to Pathological States? Life (Basel) 2020; 10:E289. [PMID: 33227899 PMCID: PMC7699229 DOI: 10.3390/life10110289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/10/2020] [Accepted: 11/16/2020] [Indexed: 01/04/2023] Open
Abstract
The property of molecular chaperones to dissolve protein aggregates of Parkinson-related α-synuclein has been known for some time. Recent findings point to an even more active role of molecular chaperones preventing the transformation of α-synuclein into pathological states subsequently leading to the formation of Lewy bodies, intracellular inclusions containing protein aggregates as well as broken organelles found in the brains of Parkinson's patients. In parallel, a short motif around Tyr39 was identified as being crucial for the aggregation of α-synuclein. Interestingly, this region is also one of the main segments in contact with a diverse pool of molecular chaperones. Further, it could be shown that the inhibition of the chaperone:α-synuclein interaction leads to a binding of α-synuclein to mitochondria, which could also be shown to lead to mitochondrial membrane disruption as well as the possible proteolytic processing of α-synuclein by mitochondrial proteases. Here, we will review the current knowledge on the role of molecular chaperones in the regulation of physiological functions as well as the direct consequences of impairing these interactions-i.e., leading to enhanced mitochondrial interaction and consequential mitochondrial breakage, which might mark the initial stages of the structural transition of α-synuclein towards its pathological states.
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Affiliation(s)
- Emelie E. Aspholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Göteborg, Sweden;
| | - Irena Matečko-Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Göteborg, Sweden;
- Department of Psychiatry and Neurochemistry, University of Gothenburg, 40530 Göteborg, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Göteborg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 40530 Göteborg, Sweden;
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41
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Conibear AC. Deciphering protein post-translational modifications using chemical biology tools. Nat Rev Chem 2020; 4:674-695. [PMID: 37127974 DOI: 10.1038/s41570-020-00223-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
Proteins carry out a wide variety of catalytic, regulatory, signalling and structural functions in living systems. Following their assembly on ribosomes and throughout their lifetimes, most eukaryotic proteins are modified by post-translational modifications; small functional groups and complex biomolecules are conjugated to amino acid side chains or termini, and the protein backbone is cleaved, spliced or cyclized, to name just a few examples. These modifications modulate protein activity, structure, location and interactions, and, thereby, control many core biological processes. Aberrant post-translational modifications are markers of cellular stress or malfunction and are implicated in several diseases. Therefore, gaining an understanding of which proteins are modified, at which sites and the resulting biological consequences is an important but complex challenge requiring interdisciplinary approaches. One of the key challenges is accessing precisely modified proteins to assign functional consequences to specific modifications. Chemical biologists have developed a versatile set of tools for accessing specifically modified proteins by applying robust chemistries to biological molecules and developing strategies for synthesizing and ligating proteins. This Review provides an overview of these tools, with selected recent examples of how they have been applied to decipher the roles of a variety of protein post-translational modifications. Relative advantages and disadvantages of each of the techniques are discussed, highlighting examples where they are used in combination and have the potential to address new frontiers in understanding complex biological processes.
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42
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Zhao K, Lim YJ, Liu Z, Long H, Sun Y, Hu JJ, Zhao C, Tao Y, Zhang X, Li D, Li YM, Liu C. Parkinson's disease-related phosphorylation at Tyr39 rearranges α-synuclein amyloid fibril structure revealed by cryo-EM. Proc Natl Acad Sci U S A 2020; 117:20305-20315. [PMID: 32737160 PMCID: PMC7443891 DOI: 10.1073/pnas.1922741117] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Posttranslational modifications (PTMs) of α-synuclein (α-syn), e.g., phosphorylation, play an important role in modulating α-syn pathology in Parkinson's disease (PD) and α-synucleinopathies. Accumulation of phosphorylated α-syn fibrils in Lewy bodies and Lewy neurites is the histological hallmark of these diseases. However, it is unclear how phosphorylation relates to α-syn pathology. Here, by combining chemical synthesis and bacterial expression, we obtained homogeneous α-syn fibrils with site-specific phosphorylation at Y39, which exhibits enhanced neuronal pathology in rat primary cortical neurons. We determined the cryo-electron microscopy (cryo-EM) structure of the pY39 α-syn fibril, which reveals a fold of α-syn with pY39 in the center of the fibril core forming an electrostatic interaction network with eight charged residues in the N-terminal region of α-syn. This structure composed of residues 1 to 100 represents the largest α-syn fibril core determined so far. This work provides structural understanding on the pathology of the pY39 α-syn fibril and highlights the importance of PTMs in defining the polymorphism and pathology of amyloid fibrils in neurodegenerative diseases.
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Affiliation(s)
- Kun Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yeh-Jun Lim
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, 100084 Beijing, China
| | - Zhenying Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Houfang Long
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yunpeng Sun
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jin-Jian Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, 100084 Beijing, China
| | - Chunyu Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Youqi Tao
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xing Zhang
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058 Hangzhou, China
- Department of Biophysics, Zhejiang University School of Medicine, 310058 Hangzhou, China
- Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, 310058 Hangzhou, China
| | - Dan Li
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, 100084 Beijing, China;
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China;
- University of Chinese Academy of Sciences, 100049 Beijing, China
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Karim MR, Liao EE, Kim J, Meints J, Martinez HM, Pletnikova O, Troncoso JC, Lee MK. α-Synucleinopathy associated c-Abl activation causes p53-dependent autophagy impairment. Mol Neurodegener 2020; 15:27. [PMID: 32299471 PMCID: PMC7164361 DOI: 10.1186/s13024-020-00364-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Studies link c-Abl activation with the accumulation of pathogenic α-synuclein (αS) and neurodegeneration in Parkinson's disease (PD). Currently, c-Abl, a tyrosine kinase activated by cellular stress, is thought to promote αS pathology by either directly phosphorylating αS or by causing autophagy deficits. METHODS αS overexpressing transgenic (Tg) mice were used in this study. A53T Tg mice that express high levels of human mutant A53TαS under the control of prion protein promoter. Two different approaches were used in this study. Natural aging and seeding model of synucleinopathy. In seeding model, intracortical/intrastriatal (IC/IS) stereotaxic injection of toxic lysates was done using tissue lysates from end-stage symptomatic mice. In this study, nilotinib and pifithrin-α was used as a c-Abl and p53 inhibitor, respectively. Both Tg and non-transgenic (nTg) mice from each group were subjected to nilotinib (10 mg/kg) or vehicle (DMSO) treatment. Frozen brain tissues from PD and control human cases were analyzed. In vitro cells study was implied for c-Abl/p53 genetic manipulation to uncover signal transduction. RESULTS Herein, we show that the pathologic effects of c-Abl in PD also involve activation of p53, as c-Abl activation in a transgenic mouse model of α-synucleinopathy (TgA53T) and human PD cases are associated with the increased p53 activation. Significantly, active p53 in TgA53T neurons accumulates in the cytosol, which may lead to inhibition of autophagy. Thus, we hypothesized that c-Abl-dependent p53 activation contributes to autophagy impairment in α-synucleinopathy. In support of the hypothesis, we show that c-Abl activation is sufficient to inhibit autophagy in p53-dependent manner. Moreover, inhibition of either c-Abl, using nilotinib, or p53, using pifithrin-α, was sufficient to increase autophagic flux in neuronal cells by inducing phosphorylation of AMP-activated kinase (AMPK), ULK1 activation, and down-regulation of mTORC1 signaling. Finally, we show that pharmacological attenuation of c-Abl activity by nilotinib treatment in the TgA53T mouse model reduces activation of p53, stimulates autophagy, decreases accumulation αS pathology, and delays disease onset. CONCLUSION Collectively, our data show that c-Abl activation by α-synucleinopathy causes p53 dependent autophagy deficits and both c-Abl and p53 represent therapeutic target for PD.
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Affiliation(s)
- Md. Razaul Karim
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55414 USA
| | - Elly E. Liao
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55414 USA
| | - Jaekwang Kim
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55414 USA
- Present Address: Department of Neural Development and Disease, Korea Brain Research Institute (KBRI), Daegu, 41068 South Korea
| | - Joyce Meints
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55414 USA
| | | | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Juan C. Troncoso
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Michael K. Lee
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55414 USA
- Institute for Translational Neuroscience, University of Minnesota, 2101 6th Street SE, Minneapolis, MN 55414 USA
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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45
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Pan B, Rhoades E, Petersson EJ. Chemoenzymatic Semisynthesis of Phosphorylated α-Synuclein Enables Identification of a Bidirectional Effect on Fibril Formation. ACS Chem Biol 2020; 15:640-645. [PMID: 32065743 DOI: 10.1021/acschembio.9b01038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Post-translational modifications (PTMs) impact the pathological aggregation of α-synuclein (αS), a hallmark of Parkinson's disease (PD). Here, we synthesize αS phosphorylated at tyrosine 39 (pY39) through a novel route using in vitro enzymatic phosphorylation of a fragment followed by ligation to form the full-length protein. We can execute this synthesis in combination with unnatural amino acid mutagenesis to include two fluorescent labels for Förster resonance energy transfer (FRET) studies. We determine the effect of pY39 on the aggregation of αS and compare our authentically phosphorylated material to the corresponding glutamate 39 "phosphomimetic." Intriguingly, we find that αS-pY39 can either accelerate or decelerate aggregation, depending on the fraction of phosphorylated protein. The αS-E39 mutant can qualitatively reproduce some, but not all, of these effects. FRET measurements and analysis of existing structures of αS help to provide an explanation for this phenomenon. Our results have important implications for the treatment of PD patients with tyrosine kinase inhibitors and highlight the importance of validating phosphomimetics through studies of authentic PTMs.
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Affiliation(s)
- Buyan Pan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Hernandez SM, Tikhonova EB, Karamyshev AL. Protein-Protein Interactions in Alpha-Synuclein Biogenesis: New Potential Targets in Parkinson's Disease. Front Aging Neurosci 2020; 12:72. [PMID: 32256340 PMCID: PMC7092629 DOI: 10.3389/fnagi.2020.00072] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
Parkinson’s disease (PD) is a debilitating neurodegenerative disorder defined by a loss of dopamine-producing neurons in the substantia nigra in the brain. It is associated with cytosolic inclusions known as Lewy bodies. The major component of Lewy bodies is aggregated alpha-synuclein. The molecular mechanism of alpha-synuclein aggregation is not known. Our conceptual model is that alpha-synuclein aggregates due to a dysregulation of its interactions with other protein partners that are required for its biogenesis. In this mini review article, we identified alpha-synuclein interactions using both current literature and predictive pathway analysis. Alterations of these interactions may be crucial elements for the molecular mechanism of the protein aggregation and related pathology in the disease. Identification of alpha-synuclein interactions provides valuable tools to understand PD pathology and find new pharmacological targets for disease treatment.
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Affiliation(s)
- Sarah M Hernandez
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Elena B Tikhonova
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
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The N-terminal Acetylation of α-Synuclein Changes the Affinity for Lipid Membranes but not the Structural Properties of the Bound State. Sci Rep 2020; 10:204. [PMID: 31937832 PMCID: PMC6959233 DOI: 10.1038/s41598-019-57023-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022] Open
Abstract
The aggregation of α-synuclein (αS), a protein abundant at presynaptic terminals, is associated with a range of highly debilitating neurodegenerative conditions, including Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Emerging evidence indicates that the interaction of αS with lipid membranes defines both its physiological function and pathological effects. The characterisation of the modes of membrane binding by αS is therefore crucial to clarify the balance between normal and aberrant behaviour of this protein. Here we used solid-state nuclear magnetic resonance (ssNMR) spectroscopy to probe the nature of the N-terminally acetylated form of αS (NTAc-αS) bound to synaptic-like lipid vesicles. This post-translational modification is prevalent for the physiological form of αS and modulates the binding to lipid bilayers. By probing the structure, dynamics and membrane topology of NTAc-αS, we found that N-terminal acetylation does not alter significantly the conformational and topological properties of the membrane-bound state of αS, despite increasing its propensity for binding. Taken together, our data and previous characterisations of the cytosolic state of NTAc-αS clarify that the role of the N-terminal acetylation is to regulate the binding affinity of αS for synaptic vesicles without altering the structural properties of the bound state.
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Moon SP, Balana AT, Galesic A, Rakshit A, Pratt MR. Ubiquitination Can Change the Structure of the α-Synuclein Amyloid Fiber in a Site Selective Fashion. J Org Chem 2019; 85:1548-1555. [PMID: 31809571 DOI: 10.1021/acs.joc.9b02641] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Toxic amyloid aggregates are a feature of many neurodegenerative diseases. A number of biochemical and structural studies have demonstrated that not all amyloids of a given protein are equivalent but rather that an aggregating protein can form different amyloid structures or polymorphisms. Different polymorphisms can also induce different amounts of pathology and toxicity in cells and in mice, suggesting that the structural differences may play important roles in disease. However, the features that cause the formation of polymorphisms in vivo are still being uncovered. Posttranslational modifications on several amyloid forming proteins, including the Parkinson's disease causing protein α-synuclein, may be one such cause. Here, we explore whether ubiquitination can induce structural changes in α-synuclein aggregates in vitro. We used protein chemistry to first synthesize ubiquitinated analogues at three different positions using disulfide linkages. After aggregation, these linkages can be reversed, allowing us to make relative comparisons between the structures using a proteinase K assay. We find that, while ubiquitination at residue 6, 23, or 96 inhibits α-synuclein aggregation, only modification at residue 96 causes an alteration in the aggregate structure, providing further evidence that posttranslational modifications may be an important feature in amyloid polymorphism formation.
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Killinger BA, Melki R, Brundin P, Kordower JH. Endogenous alpha-synuclein monomers, oligomers and resulting pathology: let's talk about the lipids in the room. NPJ PARKINSONS DISEASE 2019; 5:23. [PMID: 31728405 PMCID: PMC6851126 DOI: 10.1038/s41531-019-0095-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022]
Abstract
Alpha-synuclein is an intrinsically disordered, highly dynamic protein that pathogenically aggregates into inclusion structures called Lewy bodies, in several neurogenerative diseases termed synucleinopathies. Despite its importance for understanding disease, the oligomerization status of alpha-synuclein in healthy cells remains unclear. Alpha-synuclein may exist predominantly as either a monomer or a variety of oligomers of different molecular weights. There is solid evidence to support both theories. Detection of apparent endogenous oligomers are intimately dependent on vesicle and lipid interactions. Here we consider the possibility that apparent endogenous alpha-synuclein oligomers are in fact conformations of membrane-bound alpha-synuclein and not a bona fide stable soluble species. This perspective posits that the formation of any alpha-synuclein oligomers within the cell is likely toxic and interconversion between monomer and oligomer is tightly controlled. This differs from the hypothesis that there is a continuum of endogenous non-toxic oligomers and they convert, through unclear mechanisms, to toxic oligomers. The distinction is important, because it clarifies the biological origin of synucleinopathy. We suggest that a monomer-only, lipid-centric view of endogenous alpha-synuclein aggregation can explain how alpha-synuclein pathology is triggered, and that the interactions between alpha-synuclein and lipids can represent a target for therapeutic intervention. This discussion is well-timed due to recent studies that show lipids are a significant component of Lewy pathology.
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Affiliation(s)
- Bryan A Killinger
- 1Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612 USA
| | - Ronald Melki
- 2CEA and Laboratory of Neurodegenerative Diseases, Institut Francois Jacob (MIRCen), CNRS, 92265 Fontenay-Aux-Roses cedex, France
| | - Patrik Brundin
- 3Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI 49503 USA
| | - Jeffrey H Kordower
- 1Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612 USA
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50
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Das T, Eliezer D. Membrane interactions of intrinsically disordered proteins: The example of alpha-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2019; 1867:879-889. [PMID: 31096049 PMCID: PMC6661188 DOI: 10.1016/j.bbapap.2019.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022]
Abstract
Peripheral membrane proteins associate reversibly with biological membranes that, compared to protein binding partners, are structurally labile and devoid of specific binding pockets. Membranes in different subcellular compartments vary primarily in their chemical composition and physical properties, and recognition of these features is therefore critical for allowing such proteins to engage their proper membrane targets. Intrinsically disordered proteins (IDPs) are well-suited to accomplish this task using highly specific and low- to moderate-affinity interactions governed by recognition principles that are both similar to and different from those that mediate the membrane interactions of rigid proteins. IDPs have also evolved multiple mechanisms to regulate membrane (and other) interactions and achieve their impressive functional diversity. Moreover, IDP-membrane interactions may have a kinetic advantage in fast processes requiring rapid control of such interactions, such as synaptic transmission or signaling. Herein we review the biophysics, regulation and functional implications of IDP-membrane interactions and include a brief overview of some of the methods that can be used to study such interactions. At each step, we use the example of alpha-synuclein, a protein involved in the pathogenesis of Parkinson's disease and one of the best characterized membrane-binding IDP, to illustrate some of the principles discussed.
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Affiliation(s)
- Tapojyoti Das
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States of America
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, United States of America.
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