1
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins. J Mol Biol 2024; 436:168592. [PMID: 38702038 DOI: 10.1016/j.jmb.2024.168592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phosphosites in NPM1 reside within signal sequences, this work suggests a mechanism of NPM1 regulation by which NPM1 phosphorylation can promote 14-3-3 binding to affect NPM1 shuttling between cell compartments. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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2
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Naoi M, Maruyama W, Shamoto-Nagai M, Riederer P. Toxic interactions between dopamine, α-synuclein, monoamine oxidase, and genes in mitochondria of Parkinson's disease. J Neural Transm (Vienna) 2024; 131:639-661. [PMID: 38196001 DOI: 10.1007/s00702-023-02730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
Parkinson's disease is characterized by its distinct pathological features; loss of dopamine neurons in the substantia nigra pars compacta and accumulation of Lewy bodies and Lewy neurites containing modified α-synuclein. Beneficial effects of L-DOPA and dopamine replacement therapy indicate dopamine deficit as one of the main pathogenic factors. Dopamine and its oxidation products are proposed to induce selective vulnerability in dopamine neurons. However, Parkinson's disease is now considered as a generalized disease with dysfunction of several neurotransmitter systems caused by multiple genetic and environmental factors. The pathogenic factors include oxidative stress, mitochondrial dysfunction, α-synuclein accumulation, programmed cell death, impaired proteolytic systems, neuroinflammation, and decline of neurotrophic factors. This paper presents interactions among dopamine, α-synuclein, monoamine oxidase, its inhibitors, and related genes in mitochondria. α-Synuclein inhibits dopamine synthesis and function. Vice versa, dopamine oxidation by monoamine oxidase produces toxic aldehydes, reactive oxygen species, and quinones, which modify α-synuclein, and promote its fibril production and accumulation in mitochondria. Excessive dopamine in experimental models modifies proteins in the mitochondrial electron transport chain and inhibits the function. α-Synuclein and familiar Parkinson's disease-related gene products modify the expression and activity of monoamine oxidase. Type A monoamine oxidase is associated with neuroprotection by an unspecific dose of inhibitors of type B monoamine oxidase, rasagiline and selegiline. Rasagiline and selegiline prevent α-synuclein fibrillization, modulate this toxic collaboration, and exert neuroprotection in experimental studies. Complex interactions between these pathogenic factors play a decisive role in neurodegeneration in PD and should be further defined to develop new therapies for Parkinson's disease.
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Affiliation(s)
- Makoto Naoi
- Department of Health and Nutritional Sciences, Faculty of Health Sciences, Aichi Gakuin University, 12 Araike, Iwasaki-cho, Nisshin, Aichi, 320-0195, Japan.
| | - Wakako Maruyama
- Department of Health and Nutritional Sciences, Faculty of Health Sciences, Aichi Gakuin University, 12 Araike, Iwasaki-cho, Nisshin, Aichi, 320-0195, Japan
| | - Masayo Shamoto-Nagai
- Department of Health and Nutritional Sciences, Faculty of Health Sciences, Aichi Gakuin University, 12 Araike, Iwasaki-cho, Nisshin, Aichi, 320-0195, Japan
| | - Peter Riederer
- Clinical Neurochemistry, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, Würzburg, Germany
- Department of Psychiatry, University of Southern Denmark, Odense, Denmark
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3
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Vickery HR, Virta JM, Konstantinidou M, Arkin MR. Development of a NanoBRET assay for evaluation of 14-3-3σ molecular glues. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024:100165. [PMID: 38797286 DOI: 10.1016/j.slasd.2024.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
We report the development of a 384-well formatted NanoBRET assay to characterize molecular glues of 14-3-3/client interactions in living cells. The seven isoforms of 14-3-3 are dimeric hub proteins with diverse roles including transcription factor regulation and signal transduction. 14-3-3 interacts with hundreds of client proteins to regulate their function and is therefore an ideal therapeutic target when client selectivity can be achieved. We have developed the NanoBRET system for three 14-3-3σ client proteins CRAF, TAZ, and estrogen receptor α (ERα), which represent three specific binding modes. We have measured stabilization of 14-3-3σ/client complexes by molecular glues with EC50 values between 100 nM and 1 μM in cells, which align with the EC50 values calculated by fluorescence anisotropy in vitro. Developing this NanoBRET system for the hub protein 14-3-3σ allows for a streamlined approach, bypassing multiple optimization steps in the assay development process for other 14-3-3σ clients. The NanoBRET system allows for an assessment of PPI stabilization in a more physiologically relevant, cell-based environment using full-length proteins. The method is applicable to diverse protein-protein interactions (PPIs) and offers a robust platform to explore libraries of compounds for both PPI stabilizers and inhibitors.
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Affiliation(s)
- Holly R Vickery
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States
| | - Johanna M Virta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States
| | - Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco 94158, United States.
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4
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Trilling CR, Weng JH, Sharma PK, Nolte V, Wu J, Ma W, Boassa D, Taylor SS, Herberg FW. RedOx regulation of LRRK2 kinase activity by active site cysteines. NPJ Parkinsons Dis 2024; 10:75. [PMID: 38570484 PMCID: PMC10991482 DOI: 10.1038/s41531-024-00683-5] [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: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
Mutations of the human leucine-rich repeat kinase 2 (LRRK2) have been associated with both, idiopathic and familial Parkinson's disease (PD). Most of these pathogenic mutations are located in the kinase domain (KD) or GTPase domain of LRRK2. In this study we describe a mechanism in which protein kinase activity can be modulated by reversible oxidation or reduction, involving a unique pair of adjacent cysteines, the "CC" motif. Among all human protein kinases, only LRRK2 contains this "CC" motif (C2024 and C2025) in the Activation Segment (AS) of the kinase domain. In an approach combining site-directed mutagenesis, biochemical analyses, cell-based assays, and Gaussian accelerated Molecular Dynamics (GaMD) simulations we could attribute a role for each of those cysteines. We employed reducing and oxidizing agents with potential clinical relevance to investigate effects on kinase activity and microtubule docking. We find that each cysteine gives a distinct contribution: the first cysteine, C2024, is essential for LRRK2 protein kinase activity, while the adjacent cysteine, C2025, contributes significantly to redox sensitivity. Implementing thiolates (R-S-) in GaMD simulations allowed us to analyse how each of the cysteines in the "CC" motif interacts with its surrounding residues depending on its oxidation state. From our studies we conclude that oxidizing agents can downregulate kinase activity of hyperactive LRRK2 PD mutations and may provide promising tools for therapeutic strategies.
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Affiliation(s)
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, CA, USA
| | | | - Viktoria Nolte
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Wen Ma
- Department of Physics, University of Vermont, Burlington, VT, USA
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
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5
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Sharma PK, Weng JH, Manschwetus JT, Wu J, Ma W, Herberg FW, Taylor SS. Role of the leucine-rich repeat protein kinase 2 C-terminal tail in domain cross-talk. Biochem J 2024; 481:313-327. [PMID: 38305364 PMCID: PMC10903466 DOI: 10.1042/bcj20230477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/03/2024]
Abstract
Leucine-rich repeat protein kinase 2 (LRRK2) is a multi-domain protein encompassing two of biology's most critical molecular switches, a kinase and a GTPase, and mutations in LRRK2 are key players in the pathogenesis of Parkinson's disease (PD). The availability of multiple structures (full-length and truncated) has opened doors to explore intra-domain cross-talk in LRRK2. A helix extending from the WD40 domain and stably docking onto the kinase domain is common in all available structures. This C-terminal (Ct) helix is a hub of phosphorylation and organelle-localization motifs and thus serves as a multi-functional protein : protein interaction module. To examine its intra-domain interactions, we have recombinantly expressed a stable Ct motif (residues 2480-2527) and used peptide arrays to identify specific binding sites. We have identified a potential interaction site between the Ct helix and a loop in the CORB domain (CORB loop) using a combination of Gaussian accelerated molecular dynamics simulations and peptide arrays. This Ct-Motif contains two auto-phosphorylation sites (T2483 and T2524), and T2524 is a 14-3-3 binding site. The Ct helix, CORB loop, and the CORB-kinase linker together form a part of a dynamic 'CAP' that regulates the N-lobe of the kinase domain. We hypothesize that in inactive, full-length LRRK2, the Ct-helix will also mediate interactions with the N-terminal armadillo, ankyrin, and LRR domains (NTDs) and that binding of Rab substrates, PD mutations, or kinase inhibitors will unleash the NTDs.
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Affiliation(s)
- Pallavi Kaila Sharma
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
| | - Jascha T. Manschwetus
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Hessen, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
| | - Wen Ma
- Department of Physics, University of Vermont, Burlington, Vermont
| | - Friedrich W. Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Hessen, Germany
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0652, U.S.A
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation code of human nucleophosmin includes four cryptic sites for hierarchical binding of 14-3-3 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580064. [PMID: 38405961 PMCID: PMC10888825 DOI: 10.1101/2024.02.13.580064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phospho-sites in NPM1 reside within signal sequences, this work highlights a key mechanism of NPM1 regulation by which NPM1 phosphorylation promotes 14-3-3 binding to control nucleocytoplasmic shuttling. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A. Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V. Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B. Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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7
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Giusto E, Maistrello L, Iannotta L, Giusti V, Iovino L, Bandopadhyay R, Antonini A, Bubacco L, Barresi R, Plotegher N, Greggio E, Civiero L. Prospective Role of PAK6 and 14-3-3γ as Biomarkers for Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2024; 14:495-506. [PMID: 38640169 DOI: 10.3233/jpd-230402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Background Parkinson's disease is a progressive neurodegenerative disorder mainly distinguished by sporadic etiology, although a genetic component is also well established. Variants in the LRRK2 gene are associated with both familiar and sporadic disease. We have previously shown that PAK6 and 14-3-3γ protein interact with and regulate the activity of LRRK2. Objective The aim of this study is to quantify PAK6 and 14-3-3γ in plasma as reliable biomarkers for the diagnosis of both sporadic and LRRK2-linked Parkinson's disease. Methods After an initial quantification of PAK6 and 14-3-3γ expression by means of Western blot in post-mortem human brains, we verified the presence of the two proteins in plasma by using quantitative ELISA tests. We analyzed samples obtained from 39 healthy subjects, 40 patients with sporadic Parkinson's disease, 50 LRRK2-G2019S non-manifesting carriers and 31 patients with LRRK2-G2019S Parkinson's disease. Results The amount of PAK6 and 14-3-3γ is significantly different in patients with Parkinson's disease compared to healthy subjects. Moreover, the amount of PAK6 also varies with the presence of the G2019S mutation in the LRRK2 gene. Although the generalized linear models show a low association between the presence of Parkinson's disease and PAK6, the kinase could be added in a broader panel of biomarkers for the diagnosis of Parkinson's disease. Conclusions Changes of PAK6 and 14-3-3γ amount in plasma represent a shared readout for patients affected by sporadic and LRRK2-linked Parkinson's disease. Overall, they can contribute to the establishment of an extended panel of biomarkers for the diagnosis of Parkinson's disease.
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Affiliation(s)
| | | | - Lucia Iannotta
- Department of Biology, University of Padova, Padova, Italy
| | | | | | - Rina Bandopadhyay
- Reta Lila Weston Institute of Neurological Studies, UCL Queen Square Institute of Neurology, London, UK
| | - Angelo Antonini
- Padova Neuroscience Center, University of Padova, Padova, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
| | | | - Nicoletta Plotegher
- Department of Biology, University of Padova, Padova, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
| | - Elisa Greggio
- Department of Biology, University of Padova, Padova, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
| | - Laura Civiero
- IRCCS San Camillo Hospital, Venice, Italy
- Department of Biology, University of Padova, Padova, Italy
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8
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Iannotta L, Emanuele M, Favetta G, Tombesi G, Vandewynckel L, Lara Ordóñez AJ, Saliou JM, Drouyer M, Sibran W, Civiero L, Nichols RJ, Athanasopoulos PS, Kortholt A, Chartier-Harlin MC, Greggio E, Taymans JM. PAK6-mediated phosphorylation of PPP2R2C regulates LRRK2-PP2A complex formation. Front Mol Neurosci 2023; 16:1269387. [PMID: 38169846 PMCID: PMC10759229 DOI: 10.3389/fnmol.2023.1269387] [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: 07/29/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of inherited and sporadic Parkinson's disease (PD) and previous work suggests that dephosphorylation of LRRK2 at a cluster of heterologous phosphosites is associated to disease. We have previously reported subunits of the PP1 and PP2A classes of phosphatases as well as the PAK6 kinase as regulators of LRRK2 dephosphorylation. We therefore hypothesized that PAK6 may have a functional link with LRRK2's phosphatases. To investigate this, we used PhosTag gel electrophoresis with purified proteins and found that PAK6 phosphorylates the PP2A regulatory subunit PPP2R2C at position S381. While S381 phosphorylation did not affect PP2A holoenzyme formation, a S381A phosphodead PPP2R2C showed impaired binding to LRRK2. Also, PAK6 kinase activity changed PPP2R2C subcellular localization in a S381 phosphorylation-dependent manner. Finally, PAK6-mediated dephosphorylation of LRRK2 was unaffected by phosphorylation of PPP2R2C at S381, suggesting that the previously reported mechanism whereby PAK6-mediated phosphorylation of 14-3-3 proteins promotes 14-3-3-LRRK2 complex dissociation and consequent exposure of LRRK2 phosphosites for dephosphorylation is dominant. Taken together, we conclude that PAK6-mediated phosphorylation of PPP2R2C influences the recruitment of PPP2R2C to the LRRK2 complex and PPP2R2C subcellular localization, pointing to an additional mechanism in the fine-tuning of LRRK2 phosphorylation.
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Affiliation(s)
- Lucia Iannotta
- Department of Biology, University of Padova, Padua, Italy
- National Research Council, c/o Humanitas Research Hospital, Institute of Neuroscience, Rozzano, Italy
| | - Marco Emanuele
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Giulia Favetta
- Department of Biology, University of Padova, Padua, Italy
| | - Giulia Tombesi
- Department of Biology, University of Padova, Padua, Italy
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Laurine Vandewynckel
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | | | - Jean-Michel Saliou
- University of Lille, CNRS, Inserm, CHU Lille, Institute Pasteur de Lille, US 41 – UAR 2014 – PLBS, Lille, France
| | - Matthieu Drouyer
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - William Sibran
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Laura Civiero
- Department of Biology, University of Padova, Padua, Italy
- IRCSS, San Camillo Hospital, Venice, Italy
| | - R. Jeremy Nichols
- Department of Pathology, Stanford University, Stanford, CA, United States
| | | | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, Groningen, Netherlands
- YETEM-Innovative Technologies Application and Research Centre, Suleyman Demirel University West Campus, Isparta, Turkey
| | | | - Elisa Greggio
- Department of Biology, University of Padova, Padua, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padua, Italy
| | - Jean-Marc Taymans
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
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9
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Roy MJ, Surudoi MG, Kropp A, Hou J, Dai W, Hardy JM, Liang LY, Cotton TR, Lechtenberg BC, Dite TA, Ma X, Daly RJ, Patel O, Lucet IS. Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling. Nat Commun 2023; 14:3542. [PMID: 37336884 DOI: 10.1038/s41467-023-38869-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 05/16/2023] [Indexed: 06/21/2023] Open
Abstract
PEAK pseudokinases regulate cell migration, invasion and proliferation by recruiting key signaling proteins to the cytoskeleton. Despite lacking catalytic activity, alteration in their expression level is associated with several aggressive cancers. Here, we elucidate the molecular details of key PEAK signaling interactions with the adapter proteins CrkII and Grb2 and the scaffold protein 14-3-3. Our findings rationalize why the dimerization of PEAK proteins has a crucial function in signal transduction and provide biophysical and structural data to unravel binding specificity within the PEAK interactome. We identify a conserved high affinity 14-3-3 motif on PEAK3 and demonstrate its role as a molecular switch to regulate CrkII binding and signaling via Grb2. Together, our studies provide a detailed structural snapshot of PEAK interaction networks and further elucidate how PEAK proteins, especially PEAK3, act as dynamic scaffolds that exploit adapter proteins to control signal transduction in cell growth/motility and cancer.
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Affiliation(s)
- Michael J Roy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Minglyanna G Surudoi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ashleigh Kropp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jianmei Hou
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Weiwen Dai
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Joshua M Hardy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Lung-Yu Liang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Thomas R Cotton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Bernhard C Lechtenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Toby A Dite
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Xiuquan Ma
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Onisha Patel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Isabelle S Lucet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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10
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Pattanayak R, Petit CM, Yacoubian TA. 14-3-3 phosphorylation inhibits 14-3-3θ's ability to regulate LRRK2 kinase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542591. [PMID: 37398189 PMCID: PMC10312468 DOI: 10.1101/2023.05.27.542591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
LRRK2 mutations are among the most common genetic causes for Parkinson's disease (PD), and toxicity is associated with increased kinase activity. 14-3-3 proteins are key interactors that regulate LRRK2 kinase activity. Phosphorylation of the 14-3-3θ isoform at S232 is dramatically increased in human PD brains. Here we investigate the impact of 14-3-3θ phosphorylation on its ability to regulate LRRK2 kinase activity. Both wildtype and the non-phosphorylatable S232A 14-3-3θ mutant reduced the kinase activity of wildtype and G2019S LRRK2, whereas the phosphomimetic S232D 14-3-3θ mutant had minimal effects on LRRK2 kinase activity, as determined by measuring autophosphorylation at S1292 and T1503 and Rab10 phosphorylation. However, wildtype and both 14-3-3θ mutants similarly reduced the kinase activity of the R1441G LRRK2 mutant. 14-3-3θ phosphorylation did not promote global dissociation with LRRK2, as determined by co-immunoprecipitation and proximal ligation assays. 14-3-3s interact with LRRK2 at several phosphorylated serine/threonine sites, including T2524 in the C-terminal helix, which can fold back to regulate the kinase domain. Interaction between 14-3-3θ and phosphorylated T2524 LRRK2 was important for 14-3-3θ's ability to regulate kinase activity, as wildtype and S232A 14-3-3θ failed to reduce the kinase activity of G2019S/T2524A LRRK2. Molecular modeling showed that 14-3-3θ phosphorylation causes a partial rearrangement of its canonical binding pocket, thus affecting the interaction between 14-3-3θ and the C-terminus of LRRK2. We conclude that 14-3-3θ phosphorylation destabilizes the interaction of 14-3-3θ with LRRK2 at T2524, which consequently promotes LRRK2 kinase activity.
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Affiliation(s)
- Rudradip Pattanayak
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, 1719 Sixth Avenue South, Civitan International Research Building 510A, Birmingham, AL 35294, USA
| | - Chad M. Petit
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, 720 20 Street South, Kaul 452, Birmingham, AL 35294, USA
| | - Talene A. Yacoubian
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, 1719 Sixth Avenue South, Civitan International Research Building 510A, Birmingham, AL 35294, USA
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11
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Weng JH, Ma W, Wu J, Sharma PK, Silletti S, McCammon JA, Taylor S. Capturing Differences in the Regulation of LRRK2 Dynamics and Conformational States by Small Molecule Kinase Inhibitors. ACS Chem Biol 2023; 18:810-821. [PMID: 37043829 PMCID: PMC10127209 DOI: 10.1021/acschembio.2c00868] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023]
Abstract
Mutations in the human leucine rich repeat protein kinase-2 (LRRK2) create risk factors for Parkinson's disease, and pathological functions of LRRK2 are often correlated with aberrant kinase activity. Past research has focused on developing selective LRRK2 kinase inhibitors. In this study, we combined enhanced sampling simulations with HDX-MS to characterize the inhibitor-induced dynamic changes and the allosteric communications within the C-terminal domains of LRRK2, LRRK2RCKW. We find that the binding of MLi-2 (a type I kinase inhibitor) stabilizes a closed kinase conformation and reduces the global dynamics of LRRK2RCKW, leading to a more compact LRRK2RCKW structure. In contrast, the binding of Rebastinib (a type II kinase inhibitor) stabilizes an open kinase conformation, which promotes a more extended LRRK2RCKW structure. By probing the distinct effects of the type I and type II inhibitors, key interdomain interactions are found to regulate the communication between the kinase domain and the GTPase domain. The intermediate states revealed in our simulations facilitate the efforts toward in silico design of allosteric modulators that control LRRK2 conformations and potentially mediate the oligomeric states of LRRK2 and its interactions with other proteins.
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Affiliation(s)
- Jui-Hung Weng
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Wen Ma
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Jian Wu
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Pallavi Kaila Sharma
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Steve Silletti
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - J. Andrew McCammon
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Susan Taylor
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
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12
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Lau R, Hann MM, Ottmann C. Crystal structure and ligandability of the 14-3-3/pyrin interface. Biochem Biophys Res Commun 2023; 651:1-7. [PMID: 36774661 DOI: 10.1016/j.bbrc.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/05/2023]
Abstract
Overactivation of Pyrin is the cause of the inflammatory diseases Mediterranean Fever and Pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). Binding of 14-3-3 proteins reduces the pro-inflammatory activity of Pyrin, hence small molecules that stabilize the Pyrin/14-3-3 complex could convey an anti-inflammatory effect. We have solved the atomic resolution crystal structures of phosphorylated peptides derived from PyrinpS208 and PyrinpS242 - the two principle 14-3-3 binding sites in Pyrin - in complex with 14-3-3 and analyzed the ligandability of these protein-peptide interfaces by crystal-based fragment soaking. The complex between 14-3-3 and PyrinpS242 appears to be much more amenable for small-molecule binding than that of 14-3-3/PyrinpS208. Consequently, only for the 14-3-3/PyrinpS242 complex could we find an interface-binding fragment, validating protein crystallography and fragment soaking as a method to evaluate the ligandability of protein surfaces.
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Affiliation(s)
- Roxanne Lau
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ, Eindhoven, the Netherlands
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ, Eindhoven, the Netherlands.
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13
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Yan Y, Jiang JY, Fu M, Wang D, Pelletier AR, Sigdel D, Ng DC, Wang W, Ping P. MIND-S is a deep-learning prediction model for elucidating protein post-translational modifications in human diseases. CELL REPORTS METHODS 2023; 3:100430. [PMID: 37056379 PMCID: PMC10088250 DOI: 10.1016/j.crmeth.2023.100430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/19/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
We present a deep-learning-based platform, MIND-S, for protein post-translational modification (PTM) predictions. MIND-S employs a multi-head attention and graph neural network and assembles a 15-fold ensemble model in a multi-label strategy to enable simultaneous prediction of multiple PTMs with high performance and computation efficiency. MIND-S also features an interpretation module, which provides the relevance of each amino acid for making the predictions and is validated with known motifs. The interpretation module also captures PTM patterns without any supervision. Furthermore, MIND-S enables examination of mutation effects on PTMs. We document a workflow, its applications to 26 types of PTMs of two datasets consisting of ∼50,000 proteins, and an example of MIND-S identifying a PTM-interrupting SNP with validation from biological data. We also include use case analyses of targeted proteins. Taken together, we have demonstrated that MIND-S is accurate, interpretable, and efficient to elucidate PTM-relevant biological processes in health and diseases.
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Affiliation(s)
- Yu Yan
- NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
- Medical Informatics Program, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
| | - Jyun-Yu Jiang
- Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA
| | - Mingzhou Fu
- Medical Informatics Program, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Ding Wang
- NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
- Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
| | - Alexander R. Pelletier
- NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
- Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
- Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA
| | - Dibakar Sigdel
- NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
- Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
| | - Dominic C.M. Ng
- NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
- Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
| | - Wei Wang
- NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
- Medical Informatics Program, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA
| | - Peipei Ping
- NIH BRIDGE2AI Center at UCLA & NHLBI Integrated Cardiovascular Data Science Training Program at UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
- Medical Informatics Program, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Physiology, UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr., Los Angeles, CA 90095-1760, USA
- Scalable Analytics Institute (ScAi) at Department of Computer Science, UCLA School of Engineering, Los Angeles, CA 90095, USA
- Department of Medicine (Cardiology), UCLA School of Medicine, Suite 1-609, MRL Building, 675 Charles E. Young Dr. South, Los Angeles, CA 90095-1760, USA
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14
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Cho E, Park J, Hwang EM, Kim HW, Park JY. 14-3-3γ haploinsufficiency leads to altered dopamine pathway and Parkinson's disease-like motor incoordination in mice. Mol Brain 2023; 16:2. [PMID: 36604743 PMCID: PMC9817279 DOI: 10.1186/s13041-022-00990-z] [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: 06/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
The 14-3-3 protein family with seven isoforms found in mammals is widely expressed in the brain and plays various roles in cellular processes. Several studies have reported that 14-3-3γ, one of the 14-3-3 protein isoforms, is associated with neurological and psychiatric disorders, but the role of 14-3-3γ in the pathophysiology of brain diseases is unclear. Although studies have been conducted on the relationship between 14-3-3γ protein and Parkinson's disease (PD), a common neurodegenerative disorder with severe motor symptoms such as bradykinesia and rigidity, a direct connection remains to be elucidated. We recently showed that adult heterozygous 14-3-3γ knockout mice are hyperactive and exhibit anxiety-like behavior. In this study, we further characterized the molecular and behavioral changes in aged 14-3-3γ heterozygous mice to investigate the role of 14-3-3γ in the brain. We observed decreased dopamine levels and altered dopamine metabolism in the brains of these mice, including changes in the phosphorylation of proteins implicated in PD pathology. Furthermore, we confirmed that they displayed PD symptom-like behavioral deficits, such as impaired motor coordination and decreased ability to the nest-building activity. These findings suggest an association between 14-3-3γ dysfunction and PD pathophysiology.
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Affiliation(s)
- Eunsil Cho
- grid.222754.40000 0001 0840 2678Department of Integrated Biomedical and Life Sciences, Korea University, Seoul, 02708 Korea ,grid.222754.40000 0001 0840 2678BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841 Korea
| | - Jinsil Park
- grid.263333.40000 0001 0727 6358College of Life Sciences, Sejong University, Seoul, 05006 Korea
| | - Eun Mi Hwang
- grid.35541.360000000121053345Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, 02792 Korea
| | - Hyung Wook Kim
- grid.263333.40000 0001 0727 6358College of Life Sciences, Sejong University, Seoul, 05006 Korea
| | - Jae-Yong Park
- grid.222754.40000 0001 0840 2678Department of Integrated Biomedical and Life Sciences, Korea University, Seoul, 02708 Korea ,grid.222754.40000 0001 0840 2678BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841 Korea ,ASTRION, Seoul, 02842 Korea
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15
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Mathivanan S, Chunchagatta Lakshman PK, Singh M, Giridharan S, Sathish K, Hurakadli MA, Bharatham K, Kamariah N. Structure of a 14-3-3ε:FOXO3a pS253 Phosphopeptide Complex Reveals 14-3-3 Isoform-Specific Binding of Forkhead Box Class O Transcription Factor (FOXO) Phosphoproteins. ACS OMEGA 2022; 7:24344-24352. [PMID: 35874228 PMCID: PMC9301721 DOI: 10.1021/acsomega.2c01700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The transcriptional activity of Forkhead Box O3 (FOXO3a) is inactivated by AKT-mediated phosphorylation on Serine 253 (S253), which enables FOXO3a binding to 14-3-3. Phosphorylated FOXO3a binding to 14-3-3 facilitates the nuclear exclusion of FOXO3a, causing cancer cell proliferation. The FOXO3a/14-3-3 interaction has, therefore, emerged as an important therapeutic target. Here, we report a comprehensive analysis using fluorescence polarization, isothermal titration calorimetry, small-angle X-ray scattering, X-ray crystallography, and molecular dynamics simulations to gain molecular-level insights into the interaction of FOXO3apS253 phosphopeptide with 14-3-3ε. A high-resolution structure of the fluorophore-labeled FOXO3apS253:14-3-3ε complex revealed a distinct mode of interaction compared to other 14-3-3 phosphopeptide complexes. FOXO3apS253 phosphopeptide showed significant structural difference in the positions of the -3 and -4 Arg residues relative to pSer, compared to that of a similar phosphopeptide, FOXO1pS256 bound to 14-3-3σ. Moreover, molecular dynamics studies show that the significant structural changes and molecular interactions noticed in the crystal structure of FOXO3apS253:14-3-3ε are preserved over the course of the simulation. Thus, this study reveals structural differences between the binding to 14-3-3 isoforms of FOXO1pS256 versus FOXO3apS253, providing a framework for the rational design of isoform-specific FOXO/14-3-3 protein-protein interaction inhibitors for therapy.
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16
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Stormo AE, Shavarebi F, FitzGibbon M, Earley EM, Ahrendt H, Lum LS, Verschueren E, Swaney DL, Skibinski G, Ravisankar A, van Haren J, Davis EJ, Johnson JR, Von Dollen J, Balen C, Porath J, Crosio C, Mirescu C, Iaccarino C, Dauer WT, Nichols RJ, Wittmann T, Cox TC, Finkbeiner S, Krogan NJ, Oakes SA, Hiniker A. The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity. J Cell Biol 2022; 221:e202010065. [PMID: 35266954 PMCID: PMC8919618 DOI: 10.1083/jcb.202010065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/26/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022] Open
Abstract
Missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease (PD); however, pathways regulating LRRK2 subcellular localization, function, and turnover are not fully defined. We performed quantitative mass spectrometry-based interactome studies to identify 48 novel LRRK2 interactors, including the microtubule-associated E3 ubiquitin ligase TRIM1 (tripartite motif family 1). TRIM1 recruits LRRK2 to the microtubule cytoskeleton for ubiquitination and proteasomal degradation by binding LRRK2911-919, a nine amino acid segment within a flexible interdomain region (LRRK2853-981), which we designate the "regulatory loop" (RL). Phosphorylation of LRRK2 Ser910/Ser935 within LRRK2 RL influences LRRK2's association with cytoplasmic 14-3-3 versus microtubule-bound TRIM1. Association with TRIM1 modulates LRRK2's interaction with Rab29 and prevents upregulation of LRRK2 kinase activity by Rab29 in an E3-ligase-dependent manner. Finally, TRIM1 rescues neurite outgrowth deficits caused by PD-driving mutant LRRK2 G2019S. Our data suggest that TRIM1 is a critical regulator of LRRK2, controlling its degradation, localization, binding partners, kinase activity, and cytotoxicity.
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Affiliation(s)
- Adrienne E.D. Stormo
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Farbod Shavarebi
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Molly FitzGibbon
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Elizabeth M. Earley
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Hannah Ahrendt
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Lotus S. Lum
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Erik Verschueren
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Danielle L. Swaney
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Gaia Skibinski
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Abinaya Ravisankar
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Jeffrey van Haren
- Departments of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Emily J. Davis
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Jeffrey R. Johnson
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - John Von Dollen
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Carson Balen
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Jacob Porath
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - William T. Dauer
- Departments of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
- Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Torsten Wittmann
- Departments of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
| | - Timothy C. Cox
- Department of Oral and Craniofacial Sciences, School of Medicine, University of Missouri Kansas City, Kansas City, MO
- School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Steve Finkbeiner
- Departments of Neurology, University of California San Francisco, San Francisco, CA
- Departments of Physiology, University of California San Francisco, San Francisco, CA
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Nevan J. Krogan
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Scott A. Oakes
- Departments of Pathology, University of California San Francisco, San Francisco, CA
- Department of Pathology, University of Chicago, Chicago, IL
| | - Annie Hiniker
- Department of Pathology, University of California San Diego, San Diego, CA
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17
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LRRK2 and idiopathic Parkinson's disease. Trends Neurosci 2022; 45:224-236. [PMID: 34991886 PMCID: PMC8854345 DOI: 10.1016/j.tins.2021.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/30/2021] [Accepted: 12/09/2021] [Indexed: 12/22/2022]
Abstract
The etiology of idiopathic Parkinson's disease (iPD) is multifactorial, and both genetics and environmental exposures are risk factors. While mutations in leucine-rich repeat kinase-2 (LRRK2) that are associated with increased kinase activity are the most common cause of autosomal dominant PD, the role of LRRK2 in iPD, independent of mutations, remains uncertain. In this review, we discuss how the architecture of LRRK2 influences kinase activation and how enhanced LRRK2 substrate phosphorylation might contribute to pathogenesis. We describe how oxidative stress and endolysosomal dysfunction, both of which occur in iPD, can activate non-mutated LRRK2 to a similar degree as pathogenic mutations. Similarly, environmental toxicants that are linked epidemiologically to iPD risk can also activate LRRK2. In aggregate, current evidence suggests an important role for LRRK2 in iPD.
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18
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Weng JH, Aoto PC, Lorenz R, Wu J, Schmidt SH, Manschwetus JT, Kaila-Sharma P, Silletti S, Mathea S, Chatterjee D, Knapp S, Herberg FW, Taylor SS. LRRK2 dynamics analysis identifies allosteric control of the crosstalk between its catalytic domains. PLoS Biol 2022; 20:e3001427. [PMID: 35192607 PMCID: PMC8863276 DOI: 10.1371/journal.pbio.3001427] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The 2 major molecular switches in biology, kinases and GTPases, are both contained in the Parkinson disease-related leucine-rich repeat kinase 2 (LRRK2). Using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and molecular dynamics (MD) simulations, we generated a comprehensive dynamic allosteric portrait of the C-terminal domains of LRRK2 (LRRK2RCKW). We identified 2 helices that shield the kinase domain and regulate LRRK2 conformation and function. One helix in COR-B (COR-B Helix) tethers the COR-B domain to the αC helix of the kinase domain and faces its activation loop, while the C-terminal helix (Ct-Helix) extends from the WD40 domain and interacts with both kinase lobes. The Ct-Helix and the N-terminus of the COR-B Helix create a "cap" that regulates the N-lobe of the kinase domain. Our analyses reveal allosteric sites for pharmacological intervention and confirm the kinase domain as the central hub for conformational control.
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Affiliation(s)
- Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Phillip C. Aoto
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Robin Lorenz
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Sven H. Schmidt
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | | | - Pallavi Kaila-Sharma
- Department of Pharmacology, University of California, San Diego, California, United States of America
| | - Steve Silletti
- Department of Chemistry and Biochemistry, University of California, San Diego, California, United States of America
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deep Chatterjee
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, California, United States of America
- * E-mail:
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19
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The Roc domain of LRRK2 as a hub for protein-protein interactions: a focus on PAK6 and its impact on RAB phosphorylation. Brain Res 2022; 1778:147781. [DOI: 10.1016/j.brainres.2022.147781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022]
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20
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Helton LG, Rideout HJ, Herberg FW, Kennedy EJ. Leucine rich repeat kinase 2 (
LRRK2
) peptide modulators: Recent advances and future directions. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leah G. Helton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
| | - Hardy J. Rideout
- Center for Clinical, Experimental Surgery, and Translational Research Biomedical Research Foundation of the Academy of Athens Athens Greece
| | - Friedrich W. Herberg
- Department of Biochemistry Institute for Biology, University of Kassel Kassel Germany
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
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21
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Sluchanko NN, Tugaeva KV, Gushchin I, Remeeva A, Kovalev K, Cooley RB. Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD. Biochem Biophys Res Commun 2021; 583:100-105. [PMID: 34735870 DOI: 10.1016/j.bbrc.2021.10.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD escapes from 14-3-3, migrates to the mitochondria and initiates apoptosis. While the 14-3-3/BAD interaction represents a promising drug target, it lacks structural characterization. Among several phosphosites identified in vivo, Ser75 and Ser99 of human BAD match the consensus sequence RXXpSXP recognized by 14-3-3 and, therefore, represent canonical 14-3-3-binding sites. Yet, BAD contains other serines phosphorylatable in vivo, whose role is less understood. Here, we report a 2.36 Å crystal structure of 14-3-3ζ complexed with a BAD fragment which includes residues Ser74 and Ser75, both being substrates for protein kinases. While the BAD peptide is anchored to 14-3-3 by phosphoserine as expected, the BAD peptide was unexpectedly phosphorylated at Ser74 instead of Ser75, revealing noncanonical binding within the amphipathic groove and leading to a one-step positional shift and reorganization of the interface. This observation exemplifies plasticity of the amphipathic 14-3-3 groove in accommodating various peptides and suggests the redundancy of Ser74 and Ser75 phosphosites with respect to binding of BAD to 14-3-3.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia; European Molecular Biology Laboratory, 22607, Hamburg, Germany
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
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22
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Pathways to Parkinson's disease: a spotlight on 14-3-3 proteins. NPJ Parkinsons Dis 2021; 7:85. [PMID: 34548498 PMCID: PMC8455551 DOI: 10.1038/s41531-021-00230-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023] Open
Abstract
14-3-3s represent a family of highly conserved 30 kDa acidic proteins. 14-3-3s recognize and bind specific phospho-sequences on client partners and operate as molecular hubs to regulate their activity, localization, folding, degradation, and protein-protein interactions. 14-3-3s are also associated with the pathogenesis of several diseases, among which Parkinson's disease (PD). 14-3-3s are found within Lewy bodies (LBs) in PD patients, and their neuroprotective effects have been demonstrated in several animal models of PD. Notably, 14-3-3s interact with some of the major proteins known to be involved in the pathogenesis of PD. Here we first provide a detailed overview of the molecular composition and structural features of 14-3-3s, laying significant emphasis on their peculiar target-binding mechanisms. We then briefly describe the implication of 14-3-3s in the central nervous system and focus on their interaction with LRRK2, α-Synuclein, and Parkin, three of the major players in PD onset and progression. We finally discuss how different types of small molecules may interfere with 14-3-3s interactome, thus representing a valid strategy in the future of drug discovery.
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23
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Allosteric inhibition of LRRK2, where are we now. Biochem Soc Trans 2021; 48:2185-2194. [PMID: 33079169 PMCID: PMC7609032 DOI: 10.1042/bst20200424] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease. In recent years, it has been shown that leucine-rich repeat kinase 2 (LRRK2) has a crucial function in both familial and sporadic forms of PD. LRRK2 pathogenic mutations are thought to result in an increase in LRRK2 kinase activity. Thus, inhibiting LRRK2 kinase activity has become a main therapeutic target. Many compounds capable of inhibiting LRRK2 kinase activity with high selectivity and brain availability have been described. However, the safety of long-term use of these ATP-competitive LRRK2 kinase inhibitors has been challenged by several studies. Therefore, alternative ways of targeting LRRK2 activity will have a great benefit. In this review, we discuss the recent progress in the development of allosteric inhibitors of LRRK2, mainly via interfering with GTPase activity, and propose potential new intra and interprotein interactions targets that can lead to open doors toward new therapeutics.
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24
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Wang X, Negrou E, Maloney MT, Bondar VV, Andrews SV, Montalban M, Llapashtica C, Maciuca R, Nguyen H, Solanoy H, Arguello A, Przybyla L, Moerke NJ, Huntwork-Rodriguez S, Henry AG. Understanding LRRK2 kinase activity in preclinical models and human subjects through quantitative analysis of LRRK2 and pT73 Rab10. Sci Rep 2021; 11:12900. [PMID: 34145320 PMCID: PMC8213766 DOI: 10.1038/s41598-021-91943-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/01/2021] [Indexed: 02/08/2023] Open
Abstract
Variants in the leucine-rich repeat kinase 2 (LRRK2) gene are associated with increased risk for familial and sporadic Parkinson's disease (PD). Pathogenic variants in LRRK2, including the common variant G2019S, result in increased LRRK2 kinase activity, supporting the therapeutic potential of LRRK2 kinase inhibitors for PD. To better understand the role of LRRK2 in disease and to support the clinical development of LRRK2 inhibitors, quantitative and high-throughput assays to measure LRRK2 levels and activity are needed. We developed and applied such assays to measure the levels of LRRK2 as well as the phosphorylation of LRRK2 itself or one of its substrates, Rab10 (pT73 Rab10). We observed increased LRRK2 activity in various cellular models of disease, including iPSC-derived microglia, as well as in human subjects carrying the disease-linked variant LRRK2 G2019S. Capitalizing on the high-throughput and sensitive nature of these assays, we detected a significant reduction in LRRK2 activity in subjects carrying missense variants in LRRK2 associated with reduced disease risk. Finally, we optimized these assays to enable analysis of LRRK2 activity following inhibition in human peripheral blood mononuclear cells (PBMCs) and whole blood, demonstrating their potential utility as biomarkers to assess changes in LRRK2 expression and activity in the clinic.
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Affiliation(s)
- Xiang Wang
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Elvira Negrou
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Michael T Maloney
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Vitaliy V Bondar
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Shan V Andrews
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Manuel Montalban
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Ceyda Llapashtica
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Romeo Maciuca
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Hoang Nguyen
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Hilda Solanoy
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Annie Arguello
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Laralynne Przybyla
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | - Nathan J Moerke
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA
| | | | - Anastasia G Henry
- Denali Therapeutics, Inc., 161 Oyster Point Blvd., South San Francisco, CA, 94080, USA.
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25
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Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A 2021; 118:2100844118. [PMID: 34088839 PMCID: PMC8201809 DOI: 10.1073/pnas.2100844118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To explore how pathogenic mutations of the multidomain leucine-rich repeat kinase 2 (LRRK2) hijack its finely tuned activation process and drive Parkinson's disease (PD), we used a multitiered approach. Most mutations mimic Rab-mediated activation by "unleashing" kinase activity, and many, like the kinase inhibitor MLi-2, trap LRRK2 onto microtubules. Here we mimic activation by simply deleting the inhibitory N-terminal domains and then characterize conformational changes induced by MLi-2 and PD mutations. After confirming that LRRK2RCKW retains full kinase activity, we used hydrogen-deuterium exchange mass spectrometry to capture breathing dynamics in the presence and absence of MLi-2. Solvent-accessible regions throughout the entire protein are reduced by MLi-2 binding. With molecular dynamics simulations, we created a dynamic portrait of LRRK2RCKW and demonstrate the consequences of kinase domain mutations. Although all domains contribute to regulating kinase activity, the kinase domain, driven by the DYGψ motif, is the allosteric hub that drives LRRK2 regulation.
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26
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Azeggagh S, Berwick DC. The development of inhibitors of leucine-rich repeat kinase 2 (LRRK2) as a therapeutic strategy for Parkinson's disease: the current state of play. Br J Pharmacol 2021; 179:1478-1495. [PMID: 34050929 DOI: 10.1111/bph.15575] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/29/2022] Open
Abstract
Current therapeutic approaches for Parkinson's disease (PD) are based around treatments that alleviate symptoms but do not slow or prevent disease progression. As such, alternative strategies are needed. A promising approach is the use of molecules that reduce the function of leucine-rich repeat kinase (LRRK2). Gain-of-function mutations in LRRK2 account for a notable proportion of familial Parkinson's disease cases, and significantly, elevated LRRK2 kinase activity is reported in idiopathic Parkinson's disease. Here, we describe progress in finding therapeutically effective LRRK2 inhibitors, summarising studies that range from in vitro experiments to clinical trials. LRRK2 is a complex protein with two enzymatic activities and a myriad of functions. This creates opportunities for a rich variety of strategies and also increases the risk of unintended consequences. We comment on the strength and limitations of the different approaches and conclude that with two molecules under clinical trial and a diversity of alternative options in the pipeline, there is cause for optimism.
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Affiliation(s)
- Sonia Azeggagh
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Daniel C Berwick
- Institute of Medical and Biomedical Education, St George's, University of London, London, UK
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27
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Tugaeva KV, Hawkins DEDP, Smith JLR, Bayfield OW, Ker DS, Sysoev AA, Klychnikov OI, Antson AA, Sluchanko NN. The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins. J Mol Biol 2021; 433:166875. [PMID: 33556408 PMCID: PMC7863765 DOI: 10.1016/j.jmb.2021.166875] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association could regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, and could also hijack cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Oleg I Klychnikov
- Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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28
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Gogl G, Tugaeva KV, Eberling P, Kostmann C, Trave G, Sluchanko NN. Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms. Nat Commun 2021; 12:1677. [PMID: 33723253 PMCID: PMC7961048 DOI: 10.1038/s41467-021-21908-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The seven 14-3-3 isoforms are highly abundant human proteins encoded by similar yet distinct genes. 14-3-3 proteins recognize phosphorylated motifs within numerous human and viral proteins. Here, we analyze by X-ray crystallography, fluorescence polarization, mutagenesis and fusicoccin-mediated modulation the structural basis and druggability of 14-3-3 binding to four E6 oncoproteins of tumorigenic human papillomaviruses. 14-3-3 isoforms bind variant and mutated phospho-motifs of E6 and unrelated protein RSK1 with different affinities, albeit following an ordered affinity ranking with conserved relative KD ratios. Remarkably, 14-3-3 isoforms obey the same hierarchy when binding to most of their established targets, as supported by literature and a recent human complexome map. This knowledge allows predicting proportions of 14-3-3 isoforms engaged with phosphoproteins in various tissues. Notwithstanding their individual functions, cellular concentrations of 14-3-3 may be collectively adjusted to buffer the strongest phosphorylation outbursts, explaining their expression variations in different tissues and tumors.
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Affiliation(s)
- Gergo Gogl
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Pascal Eberling
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Camille Kostmann
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Gilles Trave
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
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29
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Wang X, Ren Y, Li J, Ji Z, Chen F, Wang X. Identification of the 14-3-3 β/α-A protein as a novel maternal peptidoglycan-binding protein that protects embryos of zebrafish against bacterial infections. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103867. [PMID: 32931839 DOI: 10.1016/j.dci.2020.103867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
14-3-3 proteins are widespread in animals, but their functions and mechanisms remain poorly defined. Here we clearly demonstrate that 14-3-3 β/α-A is a newly identified PGN-binding protein present abundantly in the eggs/embryos of zebrafish. We also show that recombinant 14-3-3 β/α-A acts as a pattern recognition receptor capable of identifying the bacterial signature molecule PGN, binding the bacteria, and functions as an antibacterial effector molecule directly killing the bacteria. Importantly, microinjection of r14-3-3 β/α-A into early embryos significantly enhanced the resistance of the embryos against pathogenic A. hydrophila challenge, and this enhanced bacterial resistance was markedly reduced by co-injection of anti-14-3-3 β/α-A antibody. Collectively, these results indicate that 14-3-3 β/α-A is a maternal PGN-binding protein that can protect the early embryos of zebrafish against pathogenic attacks, a novel role assigned to 14-3-3 β/α-A proteins. This work also provides new insights into 14-3-3 proteins that are widely distributed in various animals.
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Affiliation(s)
- Xia Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Yiqing Ren
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Jing Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China; East China University of Science and Technology, School of Biotechnology, Shanghai, 200237, China
| | - Zhe Ji
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Fushan Chen
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Xiudan Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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30
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The 14-3-3 Proteins as Important Allosteric Regulators of Protein Kinases. Int J Mol Sci 2020; 21:ijms21228824. [PMID: 33233473 PMCID: PMC7700312 DOI: 10.3390/ijms21228824] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
Phosphorylation by kinases governs many key cellular and extracellular processes, such as transcription, cell cycle progression, differentiation, secretion and apoptosis. Unsurprisingly, tight and precise kinase regulation is a prerequisite for normal cell functioning, whereas kinase dysregulation often leads to disease. Moreover, the functions of many kinases are regulated through protein–protein interactions, which in turn are mediated by phosphorylated motifs and often involve associations with the scaffolding and chaperon protein 14-3-3. Therefore, the aim of this review article is to provide an overview of the state of the art on 14-3-3-mediated kinase regulation, focusing on the most recent mechanistic insights into these important protein–protein interactions and discussing in detail both their structural aspects and functional consequences.
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31
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Taylor SS, Kaila-Sharma P, Weng JH, Aoto P, Schmidt SH, Knapp S, Mathea S, Herberg FW. Kinase Domain Is a Dynamic Hub for Driving LRRK2 Allostery. Front Mol Neurosci 2020; 13:538219. [PMID: 33122997 PMCID: PMC7573214 DOI: 10.3389/fnmol.2020.538219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
Protein kinases and GTPases are the two major molecular switches that regulate much of biology, and both of these domains are embedded within the large multi-domain Leucine-Rich Repeat Kinase 2 (LRRK2). Mutations in LRRK2 are the most common cause of familial Parkinson's disease (PD) and are also implicated in Crohn's disease. The recent Cryo-Electron Microscopy (Cryo-EM) structure of the four C-terminal domains [ROC COR KIN WD40 (RCKW)] of LRRK2 includes both of the catalytic domains. Although the important allosteric N-terminal domains are missing in the Cryo-EM structure this structure allows us to not only explore the conserved features of the kinase domain, which is trapped in an inactive and open conformation but also to observe the direct allosteric cross-talk between the two domains. To define the unique features of the kinase domain and to better understand the dynamic switch mechanism that allows LRRK2 to toggle between its inactive and active conformations, we have compared the LRRK2 kinase domain to Src, BRaf, and PKA. We also compare and contrast the two canonical glycine-rich loop motifs in LRRK2 that anchor the nucleotide: the G-Loop in protein kinases that anchors ATP and the P-Loop in GTPases that anchors GTP. The RCKW structure also provides a template for the cross-talk between the kinase and GTPase domains and brings new mechanistic insights into the physiological function of LRRK2 and how the kinase domain, along with key phosphorylation sites, can serve as an allosteric hub for mediating conformational changes.
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Affiliation(s)
- Susan S Taylor
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Pallavi Kaila-Sharma
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Jui-Hung Weng
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Phillip Aoto
- Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - Sven H Schmidt
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Sebastian Mathea
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Frankfurt, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel, Germany
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32
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Gloeckner CJ, Porras P. Guilt-by-Association - Functional Insights Gained From Studying the LRRK2 Interactome. Front Neurosci 2020; 14:485. [PMID: 32508578 PMCID: PMC7251075 DOI: 10.3389/fnins.2020.00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
The Parkinson's disease-associated Leucine-rich repeat kinase 2 (LRRK2) is a complex multi-domain protein belonging to the Roco protein family, a unique group of G-proteins. Variants of this gene are associated with an increased risk of Parkinson's disease. Besides its well-characterized enzymatic activities, conferred by its GTPase and kinase domains, and a central dimerization domain, it contains four predicted repeat domains, which are, based on their structure, commonly involved in protein-protein interactions (PPIs). In the past decades, tremendous progress has been made in determining comprehensive interactome maps for the human proteome. Knowledge of PPIs has been instrumental in assigning functions to proteins involved in human disease and helped to understand the connectivity between different disease pathways and also significantly contributed to the functional understanding of LRRK2. In addition to an increased kinase activity observed for proteins containing PD-associated variants, various studies helped to establish LRRK2 as a large scaffold protein in the interface between cytoskeletal dynamics and the vesicular transport. This review first discusses a number of specific LRRK2-associated PPIs for which a functional consequence can at least be speculated upon, and then considers the representation of LRRK2 protein interactions in public repositories, providing an outlook on open research questions and challenges in this field.
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Affiliation(s)
- Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Center for Ophthalmology, Institute for Ophthalmic Research, Core Facility for Medical Bioanalytics, University of Tübingen, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cherry Hinton, United Kingdom
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