1
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Si F, Song S, Yu R, Li Z, Wei W, Wu C. Coronavirus accessory protein ORF3 biology and its contribution to viral behavior and pathogenesis. iScience 2023; 26:106280. [PMID: 36945252 PMCID: PMC9972675 DOI: 10.1016/j.isci.2023.106280] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Coronavirus porcine epidemic diarrhea virus (PEDV) is classified in the genus Alphacoronavirus, family Coronaviridae that encodes the only accessory protein, ORF3 protein. However, how ORF3 contributes to viral pathogenicity, adaptability, and replication is obscure. In this review, we summarize current knowledge and identify gaps in many aspects of ORF3 protein in PEDV, with emphasis on its unique biological features, including membrane topology, Golgi retention mechanism, potential intrinsic disordered property, functional motifs, protein glycosylation, and codon usage phenotypes related to genetic evolution and gene expression. In addition, we propose intriguing questions related to ORF3 protein that we hope to stimulate further studies and encourage collaboration among virologists worldwide to provide constructive knowledge about the unique characteristics and biological functions of ORF3 protein, by which their potential role in clarifying viral behavior and pathogenesis can be possible.
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Affiliation(s)
- Fusheng Si
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, and Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangzhou 510640, P.R. China
| | - Ruisong Yu
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Zhen Li
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Wenqiang Wei
- Department of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, P.R. China
| | - Chao Wu
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
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2
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Feng Z, Wu X, Zhang M. Presynaptic bouton compartmentalization and postsynaptic density-mediated glutamate receptor clustering via phase separation. Neuropharmacology 2021; 193:108622. [PMID: 34051266 DOI: 10.1016/j.neuropharm.2021.108622] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/25/2021] [Accepted: 05/17/2021] [Indexed: 01/21/2023]
Abstract
Neuronal synapses encompass three compartments: presynaptic axon terminal, synaptic cleft, and postsynaptic dendrite. Each compartment contains densely packed molecular machineries that are involved in synaptic transmission. In recent years, emerging evidence indicates that the assembly of these membraneless substructures or assemblies that are not enclosed by membranes are driven by liquid-liquid phase separation. We review here recent studies that suggest the phase separation-mediated organization of these synaptic compartments. We discuss how synaptic function may be linked to its organization as biomolecular condensates. We conclude with a discussion of areas of future interest in the field for better understanding of the structural architecture of neuronal synapses and its contribution to synaptic functions.
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Affiliation(s)
- Zhe Feng
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xiandeng Wu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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3
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Krishnamurthy K, Pasinelli P. Synaptic dysfunction in amyotrophic lateral sclerosis/frontotemporal dementia: Therapeutic strategies and novel biomarkers. J Neurosci Res 2021; 99:1499-1503. [PMID: 33729613 DOI: 10.1002/jnr.24824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Karthik Krishnamurthy
- Department of Neuroscience, Jefferson Weinberg ALS Center, Vickie & Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
| | - Piera Pasinelli
- Department of Neuroscience, Jefferson Weinberg ALS Center, Vickie & Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
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4
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Boija A, Klein IA, Young RA. Biomolecular Condensates and Cancer. Cancer Cell 2021; 39:174-192. [PMID: 33417833 PMCID: PMC8721577 DOI: 10.1016/j.ccell.2020.12.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022]
Abstract
Malignant transformation is characterized by dysregulation of diverse cellular processes that have been the subject of detailed genetic, biochemical, and structural studies, but only recently has evidence emerged that many of these processes occur in the context of biomolecular condensates. Condensates are membrane-less bodies, often formed by liquid-liquid phase separation, that compartmentalize protein and RNA molecules with related functions. New insights from condensate studies portend a profound transformation in our understanding of cellular dysregulation in cancer. Here we summarize key features of biomolecular condensates, note where they have been implicated-or will likely be implicated-in oncogenesis, describe evidence that the pharmacodynamics of cancer therapeutics can be greatly influenced by condensates, and discuss some of the questions that must be addressed to further advance our understanding and treatment of cancer.
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Affiliation(s)
- Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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5
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Protachevicz PR, Iarosz KC, Caldas IL, Antonopoulos CG, Batista AM, Kurths J. Influence of Autapses on Synchronization in Neural Networks With Chemical Synapses. Front Syst Neurosci 2020; 14:604563. [PMID: 33328913 PMCID: PMC7734146 DOI: 10.3389/fnsys.2020.604563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/05/2020] [Indexed: 11/29/2022] Open
Abstract
A great deal of research has been devoted on the investigation of neural dynamics in various network topologies. However, only a few studies have focused on the influence of autapses, synapses from a neuron onto itself via closed loops, on neural synchronization. Here, we build a random network with adaptive exponential integrate-and-fire neurons coupled with chemical synapses, equipped with autapses, to study the effect of the latter on synchronous behavior. We consider time delay in the conductance of the pre-synaptic neuron for excitatory and inhibitory connections. Interestingly, in neural networks consisting of both excitatory and inhibitory neurons, we uncover that synchronous behavior depends on their synapse type. Our results provide evidence on the synchronous and desynchronous activities that emerge in random neural networks with chemical, inhibitory and excitatory synapses where neurons are equipped with autapses.
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Affiliation(s)
| | - Kelly C Iarosz
- Faculdade de Telêmaco Borba, FATEB, Telêmaco Borba, Brazil.,Graduate Program in Chemical Engineering, Federal University of Technology Paraná, Ponta Grossa, Brazil
| | - Iberê L Caldas
- Institute of Physics, University of São Paulo, São Paulo, Brazil
| | - Chris G Antonopoulos
- Department of Mathematical Sciences, University of Essex, Colchester, United Kingdom
| | - Antonio M Batista
- Institute of Physics, University of São Paulo, São Paulo, Brazil.,Department of Mathematics and Statistics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Jurgen Kurths
- Department Complexity Science, Potsdam Institute for Climate Impact Research, Potsdam, Germany.,Department of Physics, Humboldt University, Berlin, Germany.,Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia
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6
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Cinar H, Oliva R, Lin Y, Chen X, Zhang M, Chan HS, Winter R. Pressure Sensitivity of SynGAP/PSD-95 Condensates as a Model for Postsynaptic Densities and Its Biophysical and Neurological Ramifications. Chemistry 2020; 26:11024-11031. [PMID: 31910298 PMCID: PMC7496680 DOI: 10.1002/chem.201905269] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Indexed: 12/11/2022]
Abstract
Biomolecular condensates consisting of proteins and nucleic acids can serve critical biological functions, so that some condensates are referred as membraneless organelles. They can also be disease-causing, if their assembly is misregulated. A major physicochemical basis of the formation of biomolecular condensates is liquid-liquid phase separation (LLPS). In general, LLPS depends on environmental variables, such as temperature and hydrostatic pressure. The effects of pressure on the LLPS of a binary SynGAP/PSD-95 protein system mimicking postsynaptic densities, which are protein assemblies underneath the plasma membrane of excitatory synapses, were investigated. Quite unexpectedly, the model system LLPS is much more sensitive to pressure than the folded states of typical globular proteins. Phase-separated droplets of SynGAP/PSD-95 were found to dissolve into a homogeneous solution already at ten-to-hundred bar levels. The pressure sensitivity of SynGAP/PSD-95 is seen here as a consequence of both pressure-dependent multivalent interaction strength and void volume effects. Considering that organisms in the deep sea are under pressures up to about 1 kbar, this implies that deep-sea organisms have to devise means to counteract this high pressure sensitivity of biomolecular condensates to avoid harm. Intriguingly, these findings may shed light on the biophysical underpinning of pressure-related neurological disorders in terrestrial vertebrates.
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Affiliation(s)
- Hasan Cinar
- Physical Chemistry I—Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU DortmundOtto-Hahn-Strasse 4a44227DortmundGermany
| | - Rosario Oliva
- Physical Chemistry I—Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU DortmundOtto-Hahn-Strasse 4a44227DortmundGermany
| | - Yi‐Hsuan Lin
- Department of BiochemistryFaculty of MedicineUniversity of TorontoTorontoOntarioM5S 1A8Canada
- Molecular MedicineHospital for Sick ChildrenTorontoOntarioM5G 0A4Canada
| | - Xudong Chen
- Division of Life ScienceState Key Laboratory of Molecular NeuroscienceHong Kong University of Science and TechnologyClear Water BayKowloon, Hong KongChina
| | - Mingjie Zhang
- Division of Life ScienceState Key Laboratory of Molecular NeuroscienceHong Kong University of Science and TechnologyClear Water BayKowloon, Hong KongChina
| | - Hue Sun Chan
- Department of BiochemistryFaculty of MedicineUniversity of TorontoTorontoOntarioM5S 1A8Canada
| | - Roland Winter
- Physical Chemistry I—Biophysical ChemistryFaculty of Chemistry and Chemical BiologyTU DortmundOtto-Hahn-Strasse 4a44227DortmundGermany
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7
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Warnet XL, Bakke Krog H, Sevillano-Quispe OG, Poulsen H, Kjaergaard M. The C-terminal domains of the NMDA receptor: How intrinsically disordered tails affect signalling, plasticity and disease. Eur J Neurosci 2020; 54:6713-6739. [PMID: 32464691 DOI: 10.1111/ejn.14842] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 01/14/2023]
Abstract
NMDA receptors are part of the ionotropic glutamate receptor family, and are crucial for neurotransmission and memory. At the cellular level, the effects of activating these receptors include long-term potentiation (LTP) or depression (LTD). The NMDA receptor is a stringently gated cation channel permeable to Ca2+ , and it shares the molecular architecture of a tetrameric ligand-gated ion channel with the other family members. Its subunits, however, have uniquely long cytoplasmic C-terminal domains (CTDs). While the molecular gymnastics of the extracellular domains have been described in exquisite detail, much less is known about the structure and function of these CTDs. The CTDs vary dramatically in length and sequence between receptor subunits, but they all have a composition characteristic of intrinsically disordered proteins. The CTDs affect channel properties, trafficking and downstream signalling output from the receptor, and these functions are regulated by alternative splicing, protein-protein interactions, and post-translational modifications such as phosphorylation and palmitoylation. Here, we review the roles of the CTDs in synaptic plasticity with a focus on biochemical mechanisms. In total, the CTDs play a multifaceted role as a modifier of channel function, a regulator of cellular location and abundance, and signalling scaffold control the downstream signalling output.
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Affiliation(s)
- Xavier L Warnet
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark.,The Center for Proteins in Memory (PROMEMO), Aarhus University, Aarhus, Denmark
| | - Helle Bakke Krog
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark.,The Center for Proteins in Memory (PROMEMO), Aarhus University, Aarhus, Denmark
| | - Oscar G Sevillano-Quispe
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark.,The Center for Proteins in Memory (PROMEMO), Aarhus University, Aarhus, Denmark
| | - Hanne Poulsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark.,The Center for Proteins in Memory (PROMEMO), Aarhus University, Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,The Danish Research Institute for Translational Neuroscience (DANDRITE), Aarhus University, Aarhus, Denmark.,The Center for Proteins in Memory (PROMEMO), Aarhus University, Aarhus, Denmark
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8
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Patel AM, Wierda K, Thorrez L, van Putten M, De Smedt J, Ribeiro L, Tricot T, Gajjar M, Duelen R, Van Damme P, De Waele L, Goemans N, Tanganyika-de Winter C, Costamagna D, Aartsma-Rus A, van Duyvenvoorde H, Sampaolesi M, Buyse GM, Verfaillie CM. Dystrophin deficiency leads to dysfunctional glutamate clearance in iPSC derived astrocytes. Transl Psychiatry 2019; 9:200. [PMID: 31434868 PMCID: PMC6704264 DOI: 10.1038/s41398-019-0535-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) results, beside muscle degeneration in cognitive defects. As neuronal function is supported by astrocytes, which express dystrophin, we hypothesized that loss of dystrophin from DMD astrocytes might contribute to these cognitive defects. We generated cortical neuronal and astrocytic progeny from induced pluripotent stem cells (PSC) from six DMD subjects carrying different mutations and several unaffected PSC lines. DMD astrocytes displayed cytoskeletal abnormalities, defects in Ca+2 homeostasis and nitric oxide signaling. In addition, defects in glutamate clearance were identified in DMD PSC-derived astrocytes; these deficits were related to a decreased neurite outgrowth and hyperexcitability of neurons derived from healthy PSC. Read-through molecule restored dystrophin expression in DMD PSC-derived astrocytes harboring a premature stop codon mutation, corrected the defective astrocyte glutamate clearance and prevented associated neurotoxicity. We propose a role for dystrophin deficiency in defective astroglial glutamate homeostasis which initiates defects in neuronal development.
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Affiliation(s)
- Abdulsamie M. Patel
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Keimpe Wierda
- 0000000104788040grid.11486.3aCenter for Brain & Disease Research, VIB, Leuven, Belgium
| | - Lieven Thorrez
- 0000 0001 0668 7884grid.5596.fKU Leuven Department of Development and Regeneration, Campus Kulak, Kortrijk, Belgium
| | - Maaike van Putten
- 0000000089452978grid.10419.3dDepartment of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jonathan De Smedt
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Luis Ribeiro
- 0000000104788040grid.11486.3aCenter for Brain & Disease Research, VIB, Leuven, Belgium
| | - Tine Tricot
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Madhavsai Gajjar
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Robin Duelen
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium ,0000 0001 0668 7884grid.5596.fTranslational Cardiomyology Lab, Stem Cell Biology and Embryology Unit, KU Leuven, Leuven, Belgium
| | - Philip Van Damme
- 0000000104788040grid.11486.3aCenter for Brain & Disease Research, VIB, Leuven, Belgium ,0000 0001 0668 7884grid.5596.fLaboratory of Neurobiology, Department of Neuroscience, KU Leuven, Leuven, Belgium ,0000 0004 0626 3338grid.410569.fNeurology Department, University Hospitals Leuven, Leuven, Belgium
| | - Liesbeth De Waele
- 0000 0001 0668 7884grid.5596.fKU Leuven Department of Development and Regeneration, Campus Kulak, Kortrijk, Belgium ,0000 0004 0626 3338grid.410569.fDepartment of Paediatric Child Neurology, University Hospitals Leuven, Leuven, Belgium ,0000 0001 0668 7884grid.5596.fVesalius Research Center, Laboratory of Neurobiology, KU Leuven, Leuven, Belgium
| | - Nathalie Goemans
- 0000 0004 0626 3338grid.410569.fDepartment of Paediatric Child Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Christa Tanganyika-de Winter
- 0000000089452978grid.10419.3dDepartment of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Domiziana Costamagna
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium ,0000 0001 0668 7884grid.5596.fTranslational Cardiomyology Lab, Stem Cell Biology and Embryology Unit, KU Leuven, Leuven, Belgium
| | - Annemieke Aartsma-Rus
- 0000000089452978grid.10419.3dDepartment of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hermine van Duyvenvoorde
- 0000000089452978grid.10419.3dLaboratory for Diagnostic Genome Analysis, Leiden University Medical Center, Leiden, The Netherlands
| | - Maurilio Sampaolesi
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium ,0000 0001 0668 7884grid.5596.fTranslational Cardiomyology Lab, Stem Cell Biology and Embryology Unit, KU Leuven, Leuven, Belgium
| | - Gunnar M. Buyse
- 0000 0004 0626 3338grid.410569.fDepartment of Paediatric Child Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Catherine M. Verfaillie
- 0000 0001 0668 7884grid.5596.fStem Cell Institute Leuven, Dept. of Development and Regeneration, KU Leuven, Leuven, Belgium
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9
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Kiss-Tóth A, Dobson L, Péterfia B, Ángyán AF, Ligeti B, Lukács G, Gáspári Z. Occurrence of Ordered and Disordered Structural Elements in Postsynaptic Proteins Supports Optimization for Interaction Diversity. ENTROPY (BASEL, SWITZERLAND) 2019; 21:E761. [PMID: 33267475 PMCID: PMC7515291 DOI: 10.3390/e21080761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022]
Abstract
The human postsynaptic density is an elaborate network comprising thousands of proteins, playing a vital role in the molecular events of learning and the formation of memory. Despite our growing knowledge of specific proteins and their interactions, atomic-level details of their full three-dimensional structure and their rearrangements are mostly elusive. Advancements in structural bioinformatics enabled us to depict the characteristic features of proteins involved in different processes aiding neurotransmission. We show that postsynaptic protein-protein interactions are mediated through the delicate balance of intrinsically disordered regions and folded domains, and this duality is also imprinted in the amino acid sequence. We introduce Diversity of Potential Interactions (DPI), a structure and regulation based descriptor to assess the diversity of interactions. Our approach reveals that the postsynaptic proteome has its own characteristic features and these properties reliably discriminate them from other proteins of the human proteome. Our results suggest that postsynaptic proteins are especially susceptible to forming diverse interactions with each other, which might be key in the reorganization of the postsynaptic density (PSD) in molecular processes related to learning and memory.
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Affiliation(s)
- Annamária Kiss-Tóth
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
- 3in-PPCU Research Group, 2500 Esztergom, Hungary
| | - Laszlo Dobson
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Annamária F. Ángyán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Balázs Ligeti
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Gergely Lukács
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
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10
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Kurshan PT, Shen K. Synaptogenic pathways. Curr Opin Neurobiol 2019; 57:156-162. [PMID: 30986749 DOI: 10.1016/j.conb.2019.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 11/30/2022]
Abstract
During synaptogenesis, presynaptic and postsynaptic assembly are driven by diverse molecular mechanisms, mediated by intrinsic as well as extrinsic factors. How these processes are initiated and coordinated are open questions. Synapse specificity, or synaptic partner selection, is widely understood to be determined by the trans-synaptic binding of cell adhesion molecules. However, in vivo evidence that cell adhesion molecules subsequently function to initiate synapse assembly, as initially proposed, is lacking. Here, we present a summary of our current understanding of synaptogenic pathways that mediate presynaptic and postsynaptic assembly and the coordination of these processes.
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Affiliation(s)
| | - Kang Shen
- Stanford University, Department of Biology, United States; Howard Hughes Medical Institute, United States
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11
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Postsynaptic protein organization revealed by electron microscopy. Curr Opin Struct Biol 2019; 54:152-160. [PMID: 30904821 PMCID: PMC6753054 DOI: 10.1016/j.sbi.2019.02.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/02/2019] [Accepted: 02/18/2019] [Indexed: 11/21/2022]
Abstract
Neuronal synapses are key devices for transmitting and processing information in the nervous system. Synaptic plasticity, generally regarded as the cellular basis of learning and memory, involves changes of subcellular structures that take place at the nanoscale. High-resolution imaging methods, especially electron microscopy (EM), have allowed for quantitative analysis of such nanoscale structures in different types of synapses. In particular, the semi-ordered organization of neurotransmitter receptors and their interacting scaffolds in the postsynaptic density have been characterized for both excitatory and inhibitory synapses by studies using various EM techniques such as immuno-EM, electron tomography of high-pressure freezing and freeze-substituted samples, and cryo electron tomography. These techniques, in combination with new correlative approaches, will further facilitate our understanding of the molecular organization underlying diverse functions of neuronal synapses.
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12
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Das S, Amin AN, Lin YH, Chan HS. Coarse-grained residue-based models of disordered protein condensates: utility and limitations of simple charge pattern parameters. Phys Chem Chem Phys 2018; 20:28558-28574. [PMID: 30397688 DOI: 10.1039/c8cp05095c] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biomolecular condensates undergirded by phase separations of proteins and nucleic acids serve crucial biological functions. To gain physical insights into their genetic basis, we study how liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) depends on their sequence charge patterns using a continuum Langevin chain model wherein each amino acid residue is represented by a single bead. Charge patterns are characterized by the "blockiness" measure κ and the "sequence charge decoration" (SCD) parameter. Consistent with random phase approximation (RPA) theory and lattice simulations, LLPS propensity as characterized by critical temperature Tcr* increases with increasingly negative SCD for a set of sequences showing a positive correlation between κ and -SCD. Relative to RPA, the simulated sequence-dependent variation in Tcr* is often-though not always-smaller, whereas the simulated critical volume fractions are higher. However, for a set of sequences exhibiting an anti-correlation between κ and -SCD, the simulated Tcr*'s are quite insensitive to either parameter. Additionally, we find that blocky sequences that allow for strong electrostatic repulsion can lead to coexistence curves with upward concavity as stipulated by RPA, but the LLPS propensity of a strictly alternating charge sequence was likely overestimated by RPA and lattice models because interchain stabilization of this sequence requires spatial alignments that are difficult to achieve in real space. These results help delineate the utility and limitations of the charge pattern parameters and of RPA, pointing to further efforts necessary for rationalizing the newly observed subtleties.
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Affiliation(s)
- Suman Das
- Department of Biochemistry, University of Toronto, Medical Sciences Building - 5th Fl., 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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