1
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Maseko SB, Brammerloo Y, Van Molle I, Sogues A, Martin C, Gorgulla C, Plant E, Olivet J, Blavier J, Ntombela T, Delvigne F, Arthanari H, El Hajj H, Bazarbachi A, Van Lint C, Salehi-Ashtiani K, Remaut H, Ballet S, Volkov AN, Twizere JC. Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction. Antiviral Res 2023; 217:105675. [PMID: 37481039 DOI: 10.1016/j.antiviral.2023.105675] [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: 06/24/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) is the first pathogenic retrovirus discovered in human. Although HTLV-1-induced diseases are well-characterized and linked to the encoded Tax-1 oncoprotein, there is currently no strategy to target Tax-1 functions with small molecules. Here, we analyzed the binding of Tax-1 to the human homolog of the drosophila discs large tumor suppressor (hDLG1/SAP97), a multi-domain scaffolding protein involved in Tax-1-transformation ability. We have solved the structures of the PDZ binding motif (PBM) of Tax-1 in complex with the PDZ1 and PDZ2 domains of hDLG1 and assessed the binding of 10 million molecules by virtual screening. Among the 19 experimentally confirmed compounds, one systematically inhibited the Tax-1-hDLG1 interaction in different biophysical and cellular assays, as well as HTLV-1 cell-to-cell transmission in a T-cell model. Thus, our work demonstrates that interactions involving Tax-1 PDZ-domains are amenable to small-molecule inhibition, which provides a framework for the design of targeted therapies for HTLV-1-induced diseases.
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Affiliation(s)
- Sibusiso B Maseko
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Yasmine Brammerloo
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Adrià Sogues
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Julien Olivet
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | | | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hiba El Hajj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Bazarbachi
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates
| | - Han Remaut
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels Belgium.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium; Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates.
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2
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Martinez JC, Ruiz-Sanz J, Resina MJ, Montero F, Camara-Artigas A, Luque I. A calorimetric and structural analysis of cooperativity in the thermal unfolding of the PDZ tandem of human Syntenin-1. Int J Biol Macromol 2023; 242:124662. [PMID: 37119899 DOI: 10.1016/j.ijbiomac.2023.124662] [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: 02/03/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Syntenin-1 is a multidomain protein containing a central tandem of two PDZ domains flanked by two unnamed domains. Previous structural and biophysical studies show that the two PDZ domains are functional both isolated and in tandem, occurring a gain in their respective binding affinities when joined through its natural short linker. To get insight into the molecular and energetic reasons of such a gain, here, the first thermodynamic characterization of the conformational equilibrium of Syntenin-1 is presented, with special focus on its PDZ domains. These studies include the thermal unfolding of the whole protein, the PDZ-tandem construct and the two isolated PDZ domains using circular dichroism, differential scanning fluorimetry and differential scanning calorimetry. The isolated PDZ domains show low stability (ΔG < 10 kJ·mol-1) and poor cooperativity compared to the PDZ-tandem, which shows higher stability (20-30 kJ·mol-1) and a fully cooperative behaviour, with energetics similar to that previously described for archetypical PDZ domains. The high-resolution structures suggest that this remarkable increase in cooperativity is associated to strong, water-mediated, interactions at the interface between the PDZ domains, associated to nine conserved hydration regions. The low Tm value (45 °C), the anomalously high unfolding enthalpy (>400 kJ·mol-1), and native heat capacity values (above 40 kJ·K-1·mol-1), indicate that these interfacial buried waters play a relevant role in Syntenin-1 folding energetics.
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Affiliation(s)
- Jose C Martinez
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Javier Ruiz-Sanz
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - María J Resina
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Fernando Montero
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
| | - Ana Camara-Artigas
- Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento s/n, 04120 Almería, Spain.
| | - Irene Luque
- Department of Physical Chemistry, Institute of Biotechnology and Excellence Unit in Chemistry Applied to Biomedicine and Environment, Faculty of Sciences, University of Granada, Avda. Fuentenueva, s/n, 18071 Granada, Spain.
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3
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Kovács B, Zajácz-Epresi N, Gáspári Z. Ligand-dependent intra- and interdomain motions in the PDZ12 tandem regulate binding interfaces in postsynaptic density protein-95. FEBS Lett 2019; 594:887-902. [PMID: 31562775 DOI: 10.1002/1873-3468.13626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/10/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022]
Abstract
The postsynaptic density protein-95 (PSD-95) regulates synaptic plasticity through interactions mediated by its peptide-binding PDZ domains. The two N-terminal PDZ domains of PSD-95 form an autonomous structural unit, and their interdomain orientation and dynamics depend on ligand binding. To understand the mechanistic details of the effect of ligand binding, we generated conformational ensembles using available experimentally determined nuclear Overhauser effect interatomic distances and S2 order parameters. In our approach, the fast dynamics of the two domains is treated independently. We find that intradomain structural changes induced by ligand binding modulate the probability of the occurrence of specific domain-domain orientations. Our results suggest that the β2-β3 loop in the PDZ domains is a key regulatory region, which influences both intradomain motions and supramodular rearrangement.
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Affiliation(s)
- Bertalan Kovács
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary.,3in Research Group, Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Esztergom, Hungary
| | - Nóra Zajácz-Epresi
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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4
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Syntenin: PDZ Protein Regulating Signaling Pathways and Cellular Functions. Int J Mol Sci 2019; 20:ijms20174171. [PMID: 31454940 PMCID: PMC6747541 DOI: 10.3390/ijms20174171] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/22/2019] [Accepted: 08/22/2019] [Indexed: 12/29/2022] Open
Abstract
Syntenin is an adaptor-like molecule that has two adjacent tandem postsynaptic density protein 95/Discs large protein/Zonula occludens 1 (PDZ) domains. The PDZ domains of syntenin recognize multiple peptide motifs with low to moderate affinity. Many reports have indicated interactions between syntenin and a plethora of proteins. Through interactions with various proteins, syntenin regulates the architecture of the cell membrane. As a result, increases in syntenin levels induce the metastasis of tumor cells, protrusion along the neurite in neuronal cells, and exosome biogenesis in various cell types. Here, we review the updated data that support various roles for syntenin in the regulation of neuronal synapses, tumor cell invasion, and exosome control.
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Guix FX, Sannerud R, Berditchevski F, Arranz AM, Horré K, Snellinx A, Thathiah A, Saido T, Saito T, Rajesh S, Overduin M, Kumar-Singh S, Radaelli E, Corthout N, Colombelli J, Tosi S, Munck S, Salas IH, Annaert W, De Strooper B. Tetraspanin 6: a pivotal protein of the multiple vesicular body determining exosome release and lysosomal degradation of amyloid precursor protein fragments. Mol Neurodegener 2017; 12:25. [PMID: 28279219 PMCID: PMC5345265 DOI: 10.1186/s13024-017-0165-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/22/2017] [Indexed: 12/18/2022] Open
Abstract
Background The mechanisms behind Aβ-peptide accumulation in non-familial Alzheimer’s disease (AD) remain elusive. Proteins of the tetraspanin family modulate Aβ production by interacting to γ-secretase. Methods We searched for tetraspanins with altered expression in AD brains. The function of the selected tetraspanin was studied in vitro and the physiological relevance of our findings was confirmed in vivo. Results Tetraspanin-6 (TSPAN6) is increased in AD brains and overexpression in cells exerts paradoxical effects on Amyloid Precursor Protein (APP) metabolism, increasing APP-C-terminal fragments (APP-CTF) and Aβ levels at the same time. TSPAN6 affects autophagosome-lysosomal fusion slowing down the degradation of APP-CTF. TSPAN6 recruits also the cytosolic, exosome-forming adaptor syntenin which increases secretion of exosomes that contain APP-CTF. Conclusions TSPAN6 is a key player in the bifurcation between lysosomal-dependent degradation and exosome mediated secretion of APP-CTF. This corroborates the central role of the autophagosomal/lysosomal pathway in APP metabolism and shows that TSPAN6 is a crucial player in APP-CTF turnover. Electronic supplementary material The online version of this article (doi:10.1186/s13024-017-0165-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesc X Guix
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium. .,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium.
| | - Ragna Sannerud
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Fedor Berditchevski
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Amaia M Arranz
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Katrien Horré
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - An Snellinx
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Amantha Thathiah
- Department of Neurobiology, University of Pittsburgh Brain Institute, Pittsburgh Institute for Neurodegenerative Disease, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, Room 6062, 3501 Fifth Avenue, Pittsburgh, PA, 15213-3301, USA
| | - Takaomi Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, 351-0198, Saitama, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako-shi, 351-0198, Saitama, Japan
| | - Sundaresan Rajesh
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Michael Overduin
- Department of Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Canada
| | - Samir Kumar-Singh
- Molecular Pathology Group, Cell Biology & Histology, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Enrico Radaelli
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Nikky Corthout
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c. Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Sébastien Tosi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, c. Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Sebastian Munck
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Isabel H Salas
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Wim Annaert
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium.,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium
| | - Bart De Strooper
- VIB Center for Brain and Disease research - VIB, Leuven, Belgium. .,Center of Human Genetics and Leuven Institute for Neurodegenerative Diseases (LIND), KULeuven, Leuven, Gasthuisberg O&N, Belgium. .,Dementia Research Institute (DRI-UK), University College London, Queen Square, WC1N 3BG, London, UK.
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6
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Slep KC. Structure of the human discs large 1 PDZ2- adenomatous polyposis coli cytoskeletal polarity complex: insight into peptide engagement and PDZ clustering. PLoS One 2012; 7:e50097. [PMID: 23185543 PMCID: PMC3501478 DOI: 10.1371/journal.pone.0050097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/19/2012] [Indexed: 12/20/2022] Open
Abstract
The membrane associated guanylate kinase (MAGUK) family member, human Discs Large 1 (hDlg1) uses a PDZ domain array to interact with the polarity determinant, the Adenomatous Polyposis Coli (APC) microtubule plus end binding protein. The hDLG1-APC complex mediates a dynamic attachment between microtubule plus ends and polarized cortical determinants in epithelial cells, stem cells, and neuronal synapses. Using its multi-domain architecture, hDlg1 both scaffolds and regulates the polarity factors it engages. Molecular details underlying the hDlg1-APC interaction and insight into how the hDlg1 PDZ array may cluster and regulate its binding factors remain to be determined. Here, I present the crystal structure of the hDlg1 PDZ2-APC complex and the molecular determinants that mediate APC binding. The hDlg1 PDZ2-APC complex also provides insight into potential modes of ligand-dependent PDZ domain clustering that may parallel Dlg scaffold regulatory mechanisms. The hDlg1 PDZ2-APC complex presented here represents a core biological complex that bridges polarized cortical determinants with the dynamic microtubule cytoskeleton.
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Affiliation(s)
- Kevin C Slep
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.
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7
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Extensions of PSD-95/discs large/ZO-1 (PDZ) domains influence lipid binding and membrane targeting of syntenin-1. FEBS Lett 2012; 586:1445-51. [DOI: 10.1016/j.febslet.2012.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 04/10/2012] [Accepted: 04/12/2012] [Indexed: 11/21/2022]
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8
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McCann JJ, Zheng L, Chiantia S, Bowen ME. Domain orientation in the N-Terminal PDZ tandem from PSD-95 is maintained in the full-length protein. Structure 2011; 19:810-20. [PMID: 21645852 DOI: 10.1016/j.str.2011.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 01/24/2011] [Accepted: 02/21/2011] [Indexed: 12/19/2022]
Abstract
Tandem PDZ domains have been suggested to form structurally independent supramodules. However, dissimilarity between crystallography and NMR models emphasize their malleable conformation. Studies in full-length scaffold proteins are needed to examine the effect of tertiary interactions within their native context. Using single-molecule fluorescence to characterize the N-terminal PDZ tandem in PSD-95, we provide the first direct evidence that PDZ tandems can be structurally independent within a full-length scaffold protein. Molecular refinement using our data converged on a single structure with an antiparallel alignment of the ligand-binding sites. Devoid of interaction partners, single-molecule conditions captured PSD-95 in its unbound, ground state. Interactions between PDZ domains could not be detected while fluctuation correlation spectroscopy showed that other conformations are dynamically sampled. We conclude that ultra-weak interactions stabilize the conformation providing a "low-relief" energy landscape that allows the domain orientation to be flipped by environmental interactions.
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Affiliation(s)
- James J McCann
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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9
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Abstract
Abstract
The granulocyte-macrophage colony-stimulating factor (GM-CSF)/interleukin (IL)–3/IL-5 receptor family regulates the production and function of myeloid cells. These cytokines signal through receptor complexes that consist of unique ligand-binding α-chains and common signaling β-chains. IL-5 is distinct from IL-3 and GM-CSF in its capacity to induce eosinophil development, however, the molecular mechanisms that generate functional diversity within this receptor family are mostly unknown. Here, we characterized the selective IL-5Rα–binding adapter protein syntenin in IL-5R function. Syntenin and IL-5Rα colocalize at the plasma membrane and in early endosomal compartments. Manipulation of syntenin expression by ectopic expression or knockdown selectively modulated IL-5R but not GM-CSF receptor signaling, and severely affected IL-5–induced eosinophil differentiation from primary human CD34+ hematopoietic progenitor cells. We found syntenin up-regulated during eosinophilopoiesis but down-regulated during neutropoiesis. Syntenin forms complexes with multiple IL-5Rα chains, suggesting that syntenin-enhanced IL-5R output may result from stabilization of an IL-5–induced oligomeric receptor complex. These data demonstrate that cytokine-specific functions can be transduced by unique receptor α-chain–associating adapter proteins.
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10
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Cierpicki T, Bielnicki J, Zheng M, Gruszczyk J, Kasterka M, Petoukhov M, Zhang A, Fernandez EJ, Svergun DI, Derewenda U, Bushweller JH, Derewenda ZS. The solution structure and dynamics of the DH-PH module of PDZRhoGEF in isolation and in complex with nucleotide-free RhoA. Protein Sci 2009; 18:2067-79. [PMID: 19670212 PMCID: PMC2786971 DOI: 10.1002/pro.219] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 07/24/2009] [Accepted: 07/27/2009] [Indexed: 12/14/2022]
Abstract
The DH-PH domain tandems of Dbl-homology guanine nucleotide exchange factors catalyze the exchange of GTP for GDP in Rho-family GTPases, and thus initiate a wide variety of cellular signaling cascades. Although several crystal structures of complexes of DH-PH tandems with cognate, nucleotide free Rho GTPases are known, they provide limited information about the dynamics of the complex and it is not clear how accurately they represent the structures in solution. We used a complementary combination of nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and hydrogen-deuterium exchange mass spectrometry (DXMS) to study the solution structure and dynamics of the DH-PH tandem of RhoA-specific exchange factor PDZRhoGEF, both in isolation and in complex with nucleotide free RhoA. We show that in solution the DH-PH tandem behaves as a rigid entity and that the mutual disposition of the DH and PH domains remains identical within experimental error to that seen in the crystal structure of the complex, thus validating the latter as an accurate model of the complex in vivo. We also show that the nucleotide-free RhoA exhibits elevated dynamics when in complex with DH-PH, a phenomenon not observed in the crystal structure, presumably due to the restraining effects of crystal contacts. The complex is readily and rapidly dissociated in the presence of both GDP and GTP nucleotides, with no evidence of intermediate ternary complexes.
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Affiliation(s)
- Tomasz Cierpicki
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Jakub Bielnicki
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Meiying Zheng
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Jakub Gruszczyk
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Marta Kasterka
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Maxim Petoukhov
- European Molecular Biology Laboratory, Hamburg OutstationD-22603 Hamburg, Germany
| | - Aming Zhang
- Department of Chemical Engineering, University of VirginiaCharlottesville, Virginia 22908
| | - Erik J Fernandez
- Department of Chemical Engineering, University of VirginiaCharlottesville, Virginia 22908
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg OutstationD-22603 Hamburg, Germany
| | - Urszula Derewenda
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
| | - Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesville, Virginia 22908
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11
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Etzkorn M, Kneuper H, Dünnwald P, Vijayan V, Krämer J, Griesinger C, Becker S, Unden G, Baldus M. Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS. Nat Struct Mol Biol 2008; 15:1031-9. [DOI: 10.1038/nsmb.1493] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 08/29/2008] [Indexed: 11/09/2022]
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12
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Beekman JM, Coffer PJ. The ins and outs of syntenin, a multifunctional intracellular adaptor protein. J Cell Sci 2008; 121:1349-55. [DOI: 10.1242/jcs.026401] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
One of the most challenging issues currently facing cell biologists is how signal specificity and compartmentalization is achieved, allowing extracellular stimulation to result in a unique and pre-defined intracellular outcome. For this to occur, intracellular components must be correctly positioned in both space and time. Adaptor molecules, which contain protein-interaction domains, are often involved in the assembly of multimeric complexes that organize intracellular signal-transduction pathways. One such protein is syntenin, a PDZ-domain-containing molecule that has a surprising variety and diversity of interaction partners. Here we assimilate and discuss current data that support a role for syntenin in regulating transmembrane-receptor trafficking, tumour-cell metastasis and neuronal-synapse function.
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Affiliation(s)
- Jeffrey M. Beekman
- Departments of Immunology and Pediatric Immunology, Wilhelmina Children's Hospital, University Medical Center, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Paul J. Coffer
- Departments of Immunology and Pediatric Immunology, Wilhelmina Children's Hospital, University Medical Center, Lundlaan 6, 3584 EA Utrecht, The Netherlands
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13
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Cierpicki T, Liang B, Tamm LK, Bushweller JH. Increasing the accuracy of solution NMR structures of membrane proteins by application of residual dipolar couplings. High-resolution structure of outer membrane protein A. J Am Chem Soc 2007; 128:6947-51. [PMID: 16719475 PMCID: PMC2527590 DOI: 10.1021/ja0608343] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure determination of membrane proteins is one of the most challenging applications of solution NMR spectroscopy. The paucity of distance information available from the highly deuterated proteins employed requires new approaches in structure determination. Here we demonstrate that significant improvement in the structure accuracy of the membrane protein OmpA can be achieved by refinement with residual dipolar couplings (RDCs). The application of charged polyacrylamide gels allowed us to obtain two alignments and accurately measure numerous heteronuclear dipolar couplings. Furthermore, we have demonstrated that using a large set of RDCs in the refinement can yield a structure with 1 A rms deviation to the backbone of the high-resolution crystal structure. Our simulations with various data sets indicate that dipolar couplings will be critical for obtaining accurate structures of membrane proteins.
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Affiliation(s)
- Tomasz Cierpicki
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908,
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908,
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908,
| | - John H. Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908,
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22906
- CORRESPONDING AUTHOR FOOTNOTE: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908; Phone: (434) 243-6409; FAX: (434) 982-1616; e-mail:
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14
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Korotkov KV, Krumm B, Bagdasarian M, Hol WGJ. Structural and functional studies of EpsC, a crucial component of the type 2 secretion system from Vibrio cholerae. J Mol Biol 2006; 363:311-21. [PMID: 16978643 DOI: 10.1016/j.jmb.2006.08.037] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 07/19/2006] [Accepted: 08/16/2006] [Indexed: 10/24/2022]
Abstract
The type 2 secretion system (T2SS) occurring in Gram-negative bacteria is composed of 12-15 different proteins which form large assemblies spanning two membranes and secreting several virulence factors in folded state across the outer membrane. The T2SS component EpsC of Vibrio cholerae plays an important role in this machinery. While anchored in the inner membrane, by far the largest part of EpsC is periplasmic, containing a so-called homology region (HR) domain and a PDZ domain. Here we report studies on the structure and function of both periplasmic domains of EpsC. The crystal structures of two variants of the PDZ domain of EpsC from V. cholerae were determined at better than 2 A resolution. Compared to the short variant, the longer variant contains an additional N-terminal helix, and reveals a significant difference in the position of helix alphaB with respect to the beta-sheet. Both our structures show that the PDZ domain of EpsC adopts a more open form than in previously reported structures of other PDZ domains. Most interestingly, in the crystals of the short EpsC-PDZ domain the peptide binding groove interacts with an alpha-helix from a neighboring subunit burying approximately 921 A2 solvent accessible surface. This makes it possible that the PDZ domain of this bacterial protein binds proteins in a manner which is altogether different from that seen in any other PDZ domain so far. We also determined that the HR domain of EpsC is primarily responsible for the interaction with the secretin EpsD, while the PDZ is not, or much less, so. This new finding, together with studies of others, leads to the suggestion that the PDZ domain of EpsC may interact with exoproteins to be secreted while the HR domain plays a key role in linking the inner-membrane sub-complex of the T2SS in V. cholerae to the outer membrane secretin.
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Affiliation(s)
- Konstantin V Korotkov
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195, USA
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15
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Latysheva N, Muratov G, Rajesh S, Padgett M, Hotchin NA, Overduin M, Berditchevski F. Syntenin-1 is a new component of tetraspanin-enriched microdomains: mechanisms and consequences of the interaction of syntenin-1 with CD63. Mol Cell Biol 2006; 26:7707-18. [PMID: 16908530 PMCID: PMC1636879 DOI: 10.1128/mcb.00849-06] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Tetraspanins are clustered in specific microdomains (named tetraspanin-enriched microdomains, or TERM) in the plasma membrane and regulate the functions of associated transmembrane receptors, including integrins and receptor tyrosine kinases. We have identified syntenin-1, a PDZ domain-containing protein, as a new component of TERM and show that syntenin-1 specifically interacts with the tetraspanin CD63. Detailed biochemical and heteronuclear magnetic resonance spectroscopy (NMR) studies have demonstrated that the interaction is mediated by the C-terminal cytoplasmic region of the tetraspanin and the PDZ domains of syntenin-1. Upon interaction, NMR chemical shift perturbations were predominantly localized to residues around the binding pocket of PDZ1, indicating a specific mode of recognition of the cytoplasmic tail of CD63. In addition, the C terminus of syntenin-1 has a stabilizing role in the CD63-syntenin-1 association, as deletion of the last 17 amino acids abolished the interaction. The CD63-syntenin-1 complex is abundant on the plasma membrane, and the elevated expression of the wild-type syntenin-1 slows down constitutive internalization of the tetraspanin. Furthermore, internalization of CD63 was completely blocked in cells expressing a syntenin-1 mutant lacking the first 100 amino acids. Previous results have shown that CD63 is internalized via AP-2-dependent mechanisms. Hence, our data indicate that syntenin-1 can counteract the AP-2-dependent internalization and identify this tandem PDZ protein as a new regulator of endocytosis.
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Affiliation(s)
- Nadya Latysheva
- CR UK Institute for Cancer Studies, The University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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