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Holfeld A, Schuster D, Sesterhenn F, Gillingham AK, Stalder P, Haenseler W, Barrio-Hernandez I, Ghosh D, Vowles J, Cowley SA, Nagel L, Khanppnavar B, Serdiuk T, Beltrao P, Korkhov VM, Munro S, Riek R, de Souza N, Picotti P. Systematic identification of structure-specific protein-protein interactions. Mol Syst Biol 2024; 20:651-675. [PMID: 38702390 PMCID: PMC11148107 DOI: 10.1038/s44320-024-00037-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis-mass spectrometry (LiP-MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP-MS detects well-characterized PPIs, including antibody-target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states.
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Affiliation(s)
- Aleš Holfeld
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dina Schuster
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Fabian Sesterhenn
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Patrick Stalder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Walther Haenseler
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- University Research Priority Program AdaBD (Adaptive Brain Circuits in Development and Learning), University of Zurich, Zurich, Switzerland
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dhiman Ghosh
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Jane Vowles
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sally A Cowley
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Luise Nagel
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Basavraj Khanppnavar
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Volodymyr M Korkhov
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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Younas N, Zafar S, Saleem T, Fernandez Flores LC, Younas A, Schmitz M, Zerr I. Differential interactome mapping of aggregation prone/prion-like proteins under stress: novel links to stress granule biology. Cell Biosci 2023; 13:221. [PMID: 38041189 PMCID: PMC10693047 DOI: 10.1186/s13578-023-01164-7] [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: 05/30/2023] [Accepted: 11/02/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Aberrant stress granules (SGs) are emerging as prime suspects in the nucleation of toxic protein aggregates. Understanding the molecular networks linked with aggregation-prone proteins (prion protein, synuclein, and tau) under stressful environments is crucial to understand pathophysiological cascades associated with these proteins. METHODS We characterized and validated oxidative stress-induced molecular network changes of endogenous aggregation-prone proteins (prion protein, synuclein, and tau) by employing immunoprecipitation coupled with mass spectrometry analysis under basal and oxidative stress conditions. We used two different cell models (SH-SY5Y: human neuroblastoma and HeLa cell line) to induce oxidative stress using a well-known inducer (sodium arsenite) of oxidative stress. RESULTS Overall, we identified 597 proteins as potential interaction partners. Our comparative interactome mapping provides comprehensive network reorganizations of three aggregation-prone hallmark proteins, establish novel interacting partners and their dysregulation, and validates that prion protein and synuclein localize in cytoplasmic SGs. Localization of prion protein and synuclein in TIA1-positive SGs provides an important link between SG pathobiology and aggregation-prone proteins. In addition, dysregulation (downregulation) of prion protein and exportin-5 protein, and translocation of exportin-5 into the nucleus under oxidative stress shed light on nucleocytoplasmic transport defects during the stress response. CONCLUSIONS The current study contributes to our understanding of stress-mediated network rearrangements and posttranslational modifications of prion/prion-like proteins. Localization of prion protein and synuclein in the cytoplasmic SGs provides an important link between stress granule pathobiology and aggregation-prone proteins. In addition, our findings demonstrate nucleocytoplasmic transport defects after oxidative stress via dysregulation and nuclear accumulation of exportin-5.
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Affiliation(s)
- Neelam Younas
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany.
| | - Saima Zafar
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tayyaba Saleem
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Leticia Camila Fernandez Flores
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Abrar Younas
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Matthias Schmitz
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Inga Zerr
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
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Somavarapu AK, Kleijwegt G, Nagaraj M, Alam P, Nielsen J, Otzen DE. Drug repurposing screens identify compounds that inhibit α-synuclein oligomers' membrane disruption and block antibody interactions. Chem Sci 2023; 14:3030-3047. [PMID: 36937574 PMCID: PMC10016340 DOI: 10.1039/d2sc05534a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Small soluble oligomers of the protein α-synuclein (αSO) have been linked to disruptions in neuronal homeostasis, contributing to the development of Parkinson's Disease (PD). While this makes αSO an obvious drug target, the development of effective therapeutics against αSO is challenged by its low abundance and structural and morphological complexity. Here, we employ two different approaches to neutralize toxic interactions made by αSOs with different cellular components. First, we use available data to identify four neuronal proteins as likely candidates for αSO interactions, namely Cfl1, Uchl1, Sirt2 and SerRS. However, despite promising results when immobilized, all 4 proteins only bind weakly to αSO in solution in microfluidic assays, making them inappropriate for screening. In contrast, the formation of stable contacts formed between αSO and vesicles consisting of anionic lipids not only mimics a likely biological role of αSO but also provided a platform to screen two small molecule libraries for disruptors of these contacts. Of the 7 best leads obtained in this way, 2 significantly impaired αSO contacts with other proteins in a sandwich ELISA assay using αSO-binding monoclonal antibodies and nanobodies. In addition, 5 of these leads suppressed α-synuclein amyloid formation. Thus, a repurposing screening that directly targets a key culprit in PD pathogenesis shows therapeutic potential.
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Affiliation(s)
- Arun Kumar Somavarapu
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14, 8000 Aarhus C Denmark
| | - Giulia Kleijwegt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14, 8000 Aarhus C Denmark
| | - Madhu Nagaraj
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14, 8000 Aarhus C Denmark
| | - Parvez Alam
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14, 8000 Aarhus C Denmark
| | - Janni Nielsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14, 8000 Aarhus C Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University Gustav Wieds Vej 14, 8000 Aarhus C Denmark
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Yoo G, Yeou S, Son JB, Shin YK, Lee NK. Cooperative inhibition of SNARE-mediated vesicle fusion by α-synuclein monomers and oligomers. Sci Rep 2021; 11:10955. [PMID: 34040104 PMCID: PMC8155056 DOI: 10.1038/s41598-021-90503-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/12/2021] [Indexed: 11/09/2022] Open
Abstract
The primary hallmark of Parkinson's disease (PD) is the generation of Lewy bodies of which major component is α-synuclein (α-Syn). Because of increasing evidence of the fundamental roles of α-Syn oligomers in disease progression, α-Syn oligomers have become potential targets for therapeutic interventions for PD. One of the potential toxicities of α-Syn oligomers is their inhibition of SNARE-mediated vesicle fusion by specifically interacting with vesicle-SNARE protein synaptobrevin-2 (Syb2), which hampers dopamine release. Here, we show that α-Syn monomers and oligomers cooperatively inhibit neuronal SNARE-mediated vesicle fusion. α-Syn monomers at submicromolar concentrations increase the fusion inhibition by α-Syn oligomers. This cooperative pathological effect stems from the synergically enhanced vesicle clustering. Based on this cooperative inhibition mechanism, we reverse the fusion inhibitory effect of α-Syn oligomers using small peptide fragments. The small peptide fragments, derivatives of α-Syn, block the binding of α-Syn oligomers to Syb2 and dramatically reverse the toxicity of α-Syn oligomers in vesicle fusion. Our findings demonstrate a new strategy for therapeutic intervention in PD and related diseases based on this specific interaction of α-Syn.
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Affiliation(s)
- Gyeongji Yoo
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Sanghun Yeou
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Jung Bae Son
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Yeon-Kyun Shin
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
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Alpha-Synuclein and Mitochondrial Dysfunction in Parkinson's Disease: The Emerging Role of VDAC. Biomolecules 2021; 11:biom11050718. [PMID: 34064816 PMCID: PMC8170894 DOI: 10.3390/biom11050718] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/05/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022] Open
Abstract
Alpha-Synuclein (αSyn) is a protein whose function is still debated, as well as its role in modulation of mitochondrial function in both physiological and pathological conditions. Mitochondrial porins or Voltage-Dependent Anion Channel (VDAC) proteins are the main gates for ADP/ATP and various substrates towards the organelle. Furthermore, they act as a mitochondrial hub for many cytosolic proteins, including αSyn. This review analyzes the main aspects of αSyn-mitochondria interaction, focusing on the role of VDAC and its emerging involvement in the pathological processes.
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Otzen DE, Morshedi D, Mohammad-Beigi H, Aliakbari F. A Triple Role for a Bilayer: Using Nanoliposomes to Cross and Protect Cellular Membranes. J Membr Biol 2021; 254:29-39. [PMID: 33427941 DOI: 10.1007/s00232-020-00159-6] [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: 10/13/2020] [Accepted: 11/12/2020] [Indexed: 11/27/2022]
Abstract
Thanks in large part to the seminal work of Steve White and his colleagues, we appreciate the "ordered complexity" of the lipid bilayer and how it impacts the incorporation of integral membrane proteins as well as more peripherally associated proteins. Steve's work also provides a vital foundation to tackle another challenge: cytotoxic oligomeric complexes which accumulate in various neurodegenerative diseases. These oligomers have a relatively fluid structure and interact with many different proteins in the cell, but their main target is thought to be the phospholipid membrane, either the plasma membrane or internal organelles such as the mitochondria. This fascinating encounter between two essentially fluid phases generates a more disordered membrane, and presumably promotes uncontrolled transport of small metal ions across the membrane barrier. Happily, this unwanted interaction may be suppressed by mobilizing the phospholipid bilayer into its own defense. Extruded nanolipoparticles (NLPs) consisting of DPPC lipids, cholesterol and PEG2000 are excellent vehicles to take up small "oligomer-bashing" hydrophobic molecules such as baicalein and transport them with increased half-life in the plasma and with markedly more efficient crossing of the blood-brain barrier. Thus the bilayer has a triple role in this account: a safe space for a reactive hydrophobic small molecule, a barrier to cross to deliver a drug payload and a target to protect against oligomer attacks. NLPs containing small hydrophobic molecules show great promise in combating neurodegenerative diseases in animal models and may serve as an example of the White approach: applying robust physical-chemical principles to deal with biological problems involving phospholipid membranes.
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Affiliation(s)
- Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK 8000, Aarhus, Denmark.
| | - Dina Morshedi
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Hossein Mohammad-Beigi
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK 8000, Aarhus, Denmark
| | - Farhang Aliakbari
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Favretto F, Baker JD, Strohäker T, Andreas LB, Blair LJ, Becker S, Zweckstetter M. The Molecular Basis of the Interaction of Cyclophilin A with α-Synuclein. Angew Chem Int Ed Engl 2020; 59:5643-5646. [PMID: 31830361 PMCID: PMC7085457 DOI: 10.1002/anie.201914878] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Indexed: 01/09/2023]
Abstract
Peptidylprolyl isomerases (PPIases) catalyze cis/trans isomerization of prolines. The PPIase CypA colocalizes with the Parkinson's disease (PD)-associated protein α-synuclein in cells and interacts with α-synuclein oligomers. Herein, we describe atomic insights into the molecular details of the α-synuclein/CypA interaction. NMR spectroscopy shows that CypA catalyzes isomerization of proline 128 in the C-terminal domain of α-synuclein. Strikingly, we reveal a second CypA-binding site formed by the hydrophobic sequence 47 GVVHGVATVA56 , termed PreNAC. The 1.38 Å crystal structure of the CypA/PreNAC complex displays a contact between alanine 53 of α-synuclein and glutamine 111 in the catalytic pocket of CypA. Mutation of alanine 53 to glutamate, as found in patients with early-onset PD, weakens the interaction of α-synuclein with CypA. Our study provides high-resolution insights into the structure of the PD-associated protein α-synuclein in complex with the most abundant cellular cyclophilin.
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Affiliation(s)
- Filippo Favretto
- Translational Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Jeremy D Baker
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL, 33613, USA
| | - Timo Strohäker
- Translational Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Loren B Andreas
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Laura J Blair
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL, 33613, USA
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Zweckstetter
- Translational Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany.,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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