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Watanabe M, Khu TM, Warren G, Shin J, Stewart CE, Roche J. Evidence of DISC1 as an arsenic binding protein and implications regarding its role as a translational activator. Front Mol Biosci 2023; 10:1308693. [PMID: 38192336 PMCID: PMC10773898 DOI: 10.3389/fmolb.2023.1308693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024] Open
Abstract
Disrupted-in-schizophrenia-1 (DISC1) is a scaffolding protein that plays a pivotal role in orchestrating signaling pathways involved in neurodevelopment, neural migration, and synaptogenesis. Among those, it has recently been reported that the role of DISC1 in the Akt/mTOR pathway can shift from a global translational repressor to a translational activator in response to oxidative stress induced by arsenic. In this study we provide evidence that DISC1 can directly bind arsenic via a C-terminal cysteine motif (C-X-C-X-C). A series of fluorescence-based binding assays were conducted with a truncated C-terminal domain construct of DISC1 and a series of single, double, and triple cysteine mutants. We found that arsenous acid, a trivalent arsenic derivative, specifically binds to the C-terminal cysteine motif of DISC1 with low micromolar affinity. All three cysteines of the motif are required for high-affinity binding. Electron microscopy experiments combined with in silico structural predictions reveal that the C-terminal of DISC1 forms an elongated tetrameric complex. The cysteine motif is consistently predicted to be located within a loop, fully exposed to solvent, providing a simple molecular framework to explain the high-affinity of DISC1 toward arsenous acid. This study sheds light on a novel functional facet of DISC1 as an arsenic binding protein and highlights its potential role as both a sensor and translational modulator within Akt/mTOR pathway.
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Affiliation(s)
- Muneaki Watanabe
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, China
| | - Tung Mei Khu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, China
| | - Grant Warren
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, China
| | - Juyoung Shin
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, China
| | - Charles E. Stewart
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, Ames, IA, United States
| | - Julien Roche
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, China
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2
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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3
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Watanabe M, Khu TM, Warren G, Shin J, Stewart CE, Roche J. Evidence of Disrupted-in Schizophrenia 1 (DISC1) as an arsenic binding protein and implications regarding its role as a translational activator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544995. [PMID: 37398111 PMCID: PMC10312692 DOI: 10.1101/2023.06.14.544995] [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
Disrupted-in-schizophrenia-1 (DISC1) is a scaffold protein that plays a pivotal role in orchestrating signaling pathways involved in neurodevelopment, neural migration, and synaptogenesis. Among those, it has recently been reported that the role DISC1 in the Akt/mTOR pathway can shift from a global translational repressor to a translational activator in response to oxidative stress induced by arsenic. In this study we are providing evidence that DISC1 can directly bind arsenic via a C-terminal cysteine motif (C-X-C-X-C). A series of fluorescence-based binding assays were conducted with a truncated C-terminal domain construct of DISC1 and a of series of single, double, and triple cysteine mutants. We found that arsenous acid, a trivalent arsenic derivative, specifically binds to the C-terminal cysteine motif of DISC1 with low micromolar affinity. All three cysteines of the motif are required for high-affinity binding. Electron microscopy experiments combined with in silico structural predictions revealed that that the C-terminal of DISC1 forms an elongated tetrameric complex. The cysteine motif is consistently predicted to be located within a loop, fully exposed to solvent, providing a simple molecular framework to explain the high-affinity of DISC1 toward arsenous acid. This study sheds light on a novel functional facet of DISC1 as an arsenic binding protein and highlights its potential role as both a sensor and translational modulator within the Akt/mTOR pathway.
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Affiliation(s)
- Muneaki Watanabe
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, United States
| | - Tung Mei Khu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, United States
| | - Grant Warren
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, United States
| | - Juyoung Shin
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, United States
| | - Charles E Stewart
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, United States
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, United States
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DiRusso CJ, Dashtiahangar M, Gilmore TD. Scaffold proteins as dynamic integrators of biological processes. J Biol Chem 2022; 298:102628. [PMID: 36273588 PMCID: PMC9672449 DOI: 10.1016/j.jbc.2022.102628] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022] Open
Abstract
Scaffold proteins act as molecular hubs for the docking of multiple proteins to organize efficient functional units for signaling cascades. Over 300 human proteins have been characterized as scaffolds, acting in a variety of signaling pathways. While the term scaffold implies a static, supportive platform, it is now clear that scaffolds are not simply inert docking stations but can undergo conformational changes that affect their dependent signaling pathways. In this review, we catalog scaffold proteins that have been shown to undergo actionable conformational changes, with a focus on the role that conformational change plays in the activity of the classic yeast scaffold STE5, as well as three human scaffold proteins (KSR, NEMO, SHANK3) that are integral to well-known signaling pathways (RAS, NF-κB, postsynaptic density). We also discuss scaffold protein conformational changes vis-à-vis liquid-liquid phase separation. Changes in scaffold structure have also been implicated in human disease, and we discuss how aberrant conformational changes may be involved in disease-related dysregulation of scaffold and signaling functions. Finally, we discuss how understanding these conformational dynamics will provide insight into the flexibility of signaling cascades and may enhance our ability to treat scaffold-associated diseases.
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Mueterthies J, Potoyan DA. Solvent Exposure and Ionic Condensation Drive Fuzzy Dimerization of Disordered Heterochromatin Protein Sequence. Biomolecules 2021; 11:915. [PMID: 34203110 PMCID: PMC8234964 DOI: 10.3390/biom11060915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 11/29/2022] Open
Abstract
Proteins with low complexity, disordered sequences are receiving increasing attention due to their central roles in the biogenesis and regulation of membraneless organelles. In eukaryotic organisms, a substantial fraction of disordered proteins reside in the nucleus, thereby facilitating the formation of nuclear bodies, nucleolus, and chromatin compartmentalization. The heterochromatin family of proteins (HP1) is an important player in driving the formation of gene silenced mesoscopic heterochromatin B compartments and pericentric regions. Recent experiments have shown that the HP1a sequence of Drosophila melanogaster can undergo liquid-liquid phase separation under both in vitro and in vivo conditions, induced by changes of the monovalent salt concentration. While the phase separation of HP1a is thought to be the mechanism underlying chromatin compartmentalization, the molecular level mechanistic picture of salt-driven phase separation of HP1a has remained poorly understood. The disordered hinge region of HP1a is seen as the driver of salt-induced condensation because of its charge enriched sequence and post-translational modifications. Here, we set out to decipher the mechanisms of salt-induced condensation of HP1a through a systematic study of salt-dependent conformations of single chains and fuzzy dimers of disordered HP1a hinge sequences. Using multiple independent all-atom simulations with and without enhanced sampling, we carry out detailed characterization of conformational ensembles of disordered HP1a chains under different ionic conditions using various polymeric and structural measures. We show that the mobile ion release, enhancement of local transient secondary structural elements, and side-chain exposure to solvent are robust trends that accompany fuzzy dimer formation. Furthermore, we find that salt-induced changes in the ensemble of conformations of HP1a disordered hinge sequence fine-tune the inter-chain vs. self-chain interactions in ways that favor fuzzy dimer formation under low salt conditions in the agreement with condensation trends seen in experiments.
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Affiliation(s)
| | - Davit A. Potoyan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA;
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