1
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Ahmadi S, Wu YS, Li M, Ip W, Lloyd-Kuzik A, Di Paola M, Du K, Xia S, Lew A, Bozoky Z, Forman-Kay J, Bear CE, Gonska T. Augmentation of Cystic Fibrosis Transmembrane Conductance Regulator Function in Human Bronchial Epithelial Cells via SLC6A14-Dependent Amino Acid Uptake. Implications for Treatment of Cystic Fibrosis. Am J Respir Cell Mol Biol 2020; 61:755-764. [PMID: 31189070 DOI: 10.1165/rcmb.2019-0094oc] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
SLC6A14-mediated l-arginine transport has been shown to augment the residual anion channel activity of the major mutant, F508del-CFTR, in the murine gastrointestinal tract. It is not yet known if this transporter augments residual and pharmacological corrected F508del-CFTR in primary airway epithelia. We sought to determine the role of l-arginine uptake via SLC6A14 in modifying F508del-CFTR channel activity in airway cells from patients with cystic fibrosis (CF). Human bronchial epithelial (HBE) cells from lung explants of patients without CF (HBE) and those with CF (CF-HBE) were used for H3-flux, airway surface liquid, and Ussing chamber studies. We used α-methyltryptophan as a specific inhibitor for SLC6A14. CFBE41o-, a commonly used CF airway cell line, was employed for studying the mechanism of the functional interaction between SLC6A14 and F508del-CFTR. SLC6A14 is functionally expressed in CF-HBE cells. l-arginine uptake via SLC6A14 augmented F508del-CFTR function at baseline and after treatment with lumacaftor. SLC6A14-mediated l-arginine uptake also increased the airway surface liquid in CF-HBE cells. Using CFBE41o cells, we showed that the positive SLC6A14 effect was mainly dependent on the nitric oxide (NO) synthase activity, nitrogen oxides, including NO, and phosphorylation by protein kinase G. These finding were confirmed in CF-HBE, as inducible NO synthase inhibition abrogated the functional interaction between SLC6A14 and pharmacological corrected F508del-CFTR. In summary, SLC6A14-mediated l-arginine transport augments residual F508del-CFTR channel function via a noncanonical, NO pathway. This effect is enhanced with increasing pharmacological rescue of F508del-CFTR to the membrane. The current study demonstrates how endogenous pathways can be used for the development of companion therapy in CF.
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Affiliation(s)
- Saumel Ahmadi
- Department of Physiology.,Programme in Molecular Medicine.,Programme in Genetics and Genome Biology, and
| | - Yu-Sheng Wu
- Department of Physiology.,Programme in Molecular Medicine
| | - Mingyuan Li
- Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wan Ip
- Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrew Lloyd-Kuzik
- Department of Physiology.,Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Kai Du
- Department of Biochemistry, and
| | - Sunny Xia
- Department of Physiology.,Programme in Molecular Medicine
| | | | | | - Julie Forman-Kay
- Department of Biochemistry, and.,Programme in Molecular Medicine
| | - Christine E Bear
- Department of Physiology.,Department of Biochemistry, and.,Programme in Molecular Medicine
| | - Tanja Gonska
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada; and.,Programme in Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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2
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Castroverde JDM, Gomes GNW, Lee TC, Forman-Kay J, Gradinaru CC. Local Chain Dynamics of Intrinsically Disordered Sic1 Protein Inferred from Fluorescence Anisotropy Decay Measurements. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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3
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Gomes G, Krzeminski M, Forman-Kay J, Gradinaru C. Global Dimensions are Decoupled from Electrostatics in the Intrinsically Disordered Protein Sic1. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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4
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Savoia A, Pluthero F, Li L, Christensen H, De Rocco D, Traivaree C, Butchart S, Curtin J, Stollar E, Forman-Kay J, Blanchette V, Kahr W. Megakaryocyte and platelet abnormalities in a patient with a W33C mutation in the conserved SH3-like domain of myosin heavy chain IIA. Thromb Haemost 2017; 102:1241-50. [DOI: 10.1160/th09-02-0119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
SummaryHeterozygous mutations in MYH9, which encodes non-muscle myosin heavy chain IIA (MHC-IIA),result in autosomal dominant inherited MYH9-related disorders characterised by macrothrombocytopenia, granulocyte inclusions, variable sensorineural deafness, cataracts and nephritis. MHC-IIA is assembled into a complex consisting of two pairs of light chains and two heavy chains, where the latter contain a neck region, SH3-like, motor and rod domains. We describe a patient with a Trp33Cys missense mutation in the SH3-like domain of MHC-IIA. Abnormal platelet function was observed using platelet aggregometry with the agonists epinephrine and adenosine diphosphate (ADP). Patient granulocytes and megakaryocytes, but not platelets, contained abnormal MHC-IIA inclusions visualised by confocal immunofluorescence or electron microscopy. Megakaryocytes grown in culture were smaller and contained hypolobulated nuclei compared to controls. Bone marrow-derived megakaryocytes revealed a preponderance of immature forms, the presence of structurally diverse inclusion bodies, and frequent emperipolesis as assessed by electron microscopy. Platelets and leukocytes contained indistinguishable amounts of total MHCIIA determined by immunoblotting. Molecular modelling studies indicated that mutation of Trp33 destabilises the interface between the SH3-like and motor domain of MHC-IIA, which is close to previously described motor domain mutations, implying an important structural and/or functional role for this region in MHC-IIA.
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5
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Gakhal AK, Jensen TJ, Bozoky Z, Roldan A, Lukacs GL, Forman-Kay J, Riordan JR, Sidhu SS. Development and characterization of synthetic antibodies binding to the cystic fibrosis conductance regulator. MAbs 2016; 8:1167-76. [PMID: 27185291 DOI: 10.1080/19420862.2016.1186320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel in the apical surface of epithelial cells in the airway and gastrointestinal tract, and mutation of CFTR is the underlying cause of cystic fibrosis. However, the precise molecular details of the structure and function of CFTR in native and disease states remains elusive and cystic fibrosis researchers are hindered by a lack of high specificity, high affinity binding reagents for use in structural and biological studies. Here, we describe a panel of synthetic antigen-binding fragments (Fabs) isolated from a phage-displayed library that are specific for intracellular domains of CFTR that include the nucleotide-binding domains (NBD1 and NBD2), the R-region, and the regulatory insertion loop of NBD1. Binding assays performed under conditions that promote the native fold of the protein demonstrated that all Fabs recognized full-length CFTR. However, only the NBD1-specific Fab recognized denatured CFTR by western blot, suggesting a conformational epitope requirement for the other Fabs. Surface plasmon resonance experiments showed that the R-region Fab binds with high affinity to both the phosphorylated and unphosphorylated R-region. In addition, NMR analysis of bound versus unbound R-region revealed a distinct conformational effect upon Fab binding. We further defined residues involved with antibody recognition using an overlapping peptide array. In summary, we describe methodology complementary to previous hybridoma-based efforts to develop antibody reagents to CFTR, and introduce a synthetic antibody panel to aid structural and biological studies.
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Affiliation(s)
- Amandeep K Gakhal
- a Donnelly Center for Cellular and Biomolecular Research , University of Toronto , Toronto , Ontario , Canada
| | - Timothy J Jensen
- b Department of Biochemistry and Biophysics , Cystic Fibrosis Treatment and Research Center, University of North Carolina , Chapel Hill , NC , USA
| | - Zoltan Bozoky
- c Program in Molecular Structure & Function , The Hospital for Sick Children , Toronto , ON , Canada.,d Department of Biochemistry , University of Toronto, Toronto , ON , Canada
| | - Ariel Roldan
- e Department of Physiology and Biochemistry , McGill University , Montreal , QC , Canada
| | - Gergely L Lukacs
- e Department of Physiology and Biochemistry , McGill University , Montreal , QC , Canada
| | - Julie Forman-Kay
- c Program in Molecular Structure & Function , The Hospital for Sick Children , Toronto , ON , Canada.,d Department of Biochemistry , University of Toronto, Toronto , ON , Canada
| | - John R Riordan
- b Department of Biochemistry and Biophysics , Cystic Fibrosis Treatment and Research Center, University of North Carolina , Chapel Hill , NC , USA
| | - Sachdev S Sidhu
- a Donnelly Center for Cellular and Biomolecular Research , University of Toronto , Toronto , Ontario , Canada
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6
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Gomes GW, Liu B, Farber P, Csizmok V, Forman-Kay J, Gradinaru CC. Electrostatics-Dependent Shape of the Intrinsically-Disordered Protein Sic1. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.3812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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7
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Zhang Z, Mazouchi A, Chong A, Forman-Kay J, Gradinaru C. The Conformations of the DrkN SH3 Domain Studied by Single Molecule Fluorescence Spectroscopy. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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8
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Dunker AK, Babu MM, Barbar E, Blackledge M, Bondos SE, Dosztányi Z, Dyson HJ, Forman-Kay J, Fuxreiter M, Gsponer J, Han KH, Jones DT, Longhi S, Metallo SJ, Nishikawa K, Nussinov R, Obradovic Z, Pappu RV, Rost B, Selenko P, Subramaniam V, Sussman JL, Tompa P, Uversky VN. What's in a name? Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered. Intrinsically Disord Proteins 2013; 1:e24157. [PMID: 28516007 PMCID: PMC5424803 DOI: 10.4161/idp.24157] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 02/26/2013] [Indexed: 02/04/2023]
Abstract
"What's in a name? That which we call a rose By any other name would smell as sweet." From "Romeo and Juliet", William Shakespeare (1594) This article opens a series of publications on disambiguation of the basic terms used in the field of intrinsically disordered proteins. We start from the beginning, namely from the explanation of what the expression "intrinsically disordered protein" actually means and why this particular term has been chosen as the common denominator for this class of proteins characterized by broad structural, dynamic and functional characteristics.
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Affiliation(s)
- A Keith Dunker
- Indiana University School of Medicine; Indianapolis, IN USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology; Cambridge, UK
| | | | | | - Sarah E Bondos
- Texas A&M Health Science Center; College Station, TX, USA
| | | | - H Jane Dyson
- The Scripps Research Institute; La Jolla, CA, USA
| | - Julie Forman-Kay
- Hospital for Sick Children and University of Toronto; Toronto, ON, Canada
| | | | - Jörg Gsponer
- University of British Columbia; Vancouver, BC Canada
| | - Kyou-Hoon Han
- Korean Research Institute of Bioscience and Biotechnology; Daejeon, Korea
| | | | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques; CNRS and Aix-Marseille Université; Marseille, France
| | | | | | - Ruth Nussinov
- National Cancer Institute; Frederick, MD USA.,Tel Aviv University; Tel Aviv, Israel
| | | | - Rohit V Pappu
- Washington University in St. Louis; St. Louis, MO USA
| | | | - Philipp Selenko
- Leibniz Institute of Molecular Pharmacology; Berlin, Germany
| | | | | | - Peter Tompa
- VIB Department of Structural Biology; Brussels, Belgium.,Vrije Universiteit Brussel; Brussels, Belgium.,Institute of Enzymology; Budapest, Hungary
| | - Vladimir N Uversky
- University of South Florida, College of Medicine; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Russia
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9
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Gradinaru C, Mazouchi A, Rauscher S, Pomes R, Forman-Kay J. The Intrinsically Unstable SH3-DRKN Protein: Compactness, Conformations and Speed. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S. In support of the BMRB. Nat Struct Mol Biol 2012; 19:854-60. [PMID: 22955930 DOI: 10.1038/nsmb.2371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- John L Markley
- University of Wisconsin-Madison, Madison, Wisconsin, USA
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Ogunjimi AA, Wiesner S, Briant DJ, Varelas X, Sicheri F, Forman-Kay J, Wrana JL. The ubiquitin binding region of the Smurf HECT domain facilitates polyubiquitylation and binding of ubiquitylated substrates. J Biol Chem 2009; 285:6308-15. [PMID: 20026602 DOI: 10.1074/jbc.m109.044537] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Mono- and polyubiquitylation of proteins are key steps in a wide range of biological processes. However, the molecular mechanisms that mediate these different events are poorly understood. Here, we employed NMR spectroscopy to map a non-covalent ubiquitin binding surface (UBS) on the Smurf ubiquitin ligase HECT domain. Analysis of mutants of the HECT UBS reveal that interfering with the UBS surface blocked Smurf-dependent degradation of its substrate RhoA in cells. In vitro analysis revealed that the UBS was not required for UbcH7-dependent charging of the HECT catalytic cysteine. Surprisingly, although the UBS was required for polyubiquitylation of both Smurf itself and the Smurf substrate RhoA, it was not required for monoubiquitylation. Furthermore, we show that mutating the UBS interfered with efficient binding of a monoubiquitylated form of RhoA to the Smurf HECT domain. Our findings suggest the UBS promotes polyubiquitylation by stabilizing ubiquitylated substrate binding to the HECT domain.
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Affiliation(s)
- Abiodun A Ogunjimi
- Center for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
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12
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Forman-Kay J, Mittag T, Baker JM, Marsh JA. Mechanisms Of Biological Regulation By Highly Dynamic Protein Complexes. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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13
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Evanics F, Kitevski JL, Bezsonova I, Forman-Kay J, Prosser RS. 19F NMR studies of solvent exposure and peptide binding to an SH3 domain. Biochim Biophys Acta Gen Subj 2006; 1770:221-30. [PMID: 17182189 DOI: 10.1016/j.bbagen.2006.10.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 10/02/2006] [Accepted: 10/23/2006] [Indexed: 11/21/2022]
Abstract
(19)F NMR was used to study topological features of the SH3 domain of Fyn tyrosine kinase for both the free protein and a complex formed with a binding peptide. Metafluorinated tyrosine was biosynthetically incorporated into each of 5 residues of the G48M mutant of the SH3 domain (i.e. residues 8, 10, 49 and 54 in addition to a single residue in the linker region to the C-terminal polyhistidine tag). Distinct (19)F NMR resonances were observed and subsequently assigned after separately introducing single phenylalanine mutations. (19)F NMR chemical shifts were dependent on protein concentration above 0.6 mM, suggestive of dimerization via the binding site in the vicinity of the tyrosine side chains. (19)F NMR spectra of Fyn SH3 were also obtained as a function of concentration of a small peptide (2-hydroxynicotinic-NH)-Arg-Ala-Leu-Pro-Pro-Leu-Pro-diaminopropionic acid -NH(2), known to interact with the canonical polyproline II (PPII) helix binding site of the SH3 domain. Based on the (19)F chemical shifts of Tyr8, Tyr49, and Tyr54, as a function of peptide concentration, an equilibrium dissociation constant of 18 +/- 4 microM was obtained. Analysis of the line widths suggested an average exchange rate, k(ex), associated with the peptide-protein two-site exchange, of 5200 +/- 600 s(-1) at a peptide concentration where 96% of the FynSH3 protein was assumed to be bound. The extent of solvent exposure of the fluorine labels was studied by a combination of solvent isotope shifts and paramagnetic effects from dissolved oxygen. Tyr54, Tyr49, Tyr10, and Tyr8, in addition to the Tyr on the C-terminal tag, appear to be fully exposed to the solvent at the metafluoro position in the absence of binding peptide. Tyr54 and, to some extent, Tyr10 become protected from the solvent in the peptide bound state, consistent with known structural data on SH3-domain peptide complexes. These results show the potential utility of (19)F-metafluorotyrosine to probe protein-protein interactions in conjunction with paramagnetic contrast agents.
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Affiliation(s)
- Ferenc Evanics
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd. North Mississauga, ON, Canada L5L 1C6
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14
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Henry PC, Kanelis V, O'Brien MC, Kim B, Gautschi I, Forman-Kay J, Schild L, Rotin D. Affinity and specificity of interactions between Nedd4 isoforms and the epithelial Na+ channel. J Biol Chem 2003; 278:20019-28. [PMID: 12654927 DOI: 10.1074/jbc.m211153200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The epithelial Na+ channel (alphabetagammaENaC) regulates salt and fluid homeostasis and blood pressure. Each ENaC subunit contains a PY motif (PPXY) that binds to the WW domains of Nedd4, a Hect family ubiquitin ligase containing 3-4 WW domains and usually a C2 domain. It has been proposed that Nedd4-2, but not Nedd4-1, isoforms can bind to and suppress ENaC activity. Here we challenge this notion and show that, instead, the presence of a unique WW domain (WW3*) in either Nedd4-2 or Nedd4-1 determines high affinity interactions and the ability to suppress ENaC. WW3* from either Nedd4-2 or Nedd4-1 binds ENaC-PY motifs equally well (e.g. Kd approximately 10 microm for alpha- or betaENaC, 3-6-fold higher affinity than WW4), as determined by intrinsic tryptophan fluorescence. Moreover, dNedd4-1, which naturally contains a WW3* instead of WW2, is able to suppress ENaC function equally well as Nedd4-2. Homology models of the WW3*.betaENaC-PY complex revealed that a Pro and Ala conserved in all WW3*, but not other Nedd4-WW domains, help form the binding pocket for PY motif prolines. Extensive contacts are formed between the betaENaC-PY motif and the Pro in WW3*, and the small Ala creates a large pocket to accommodate the peptide. Indeed, mutating the conserved Pro and Ala in WW3* reduces binding affinity 2-3-fold. Additionally, we demonstrate that mutations in PY motif residues that form contacts with the WW domain based on our previously solved structure either abolish or severely reduce binding affinity to the WW domain and that the extent of binding correlates with the level of ENaC suppression. Independently, we show that a peptide encompassing the PY motif of sgk1, previously proposed to bind to Nedd4-2 and alter its ability to regulate ENaC, does not bind (or binds poorly) the WW domains of Nedd4-2. Collectively, these results suggest that high affinity of WW domain-PY-motif interactions rather than affiliation with Nedd4-1/Nedd-2 is critical for ENaC suppression by Nedd4 proteins.
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Affiliation(s)
- Pauline C Henry
- Programme in Cell Biology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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15
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Kortemme T, Kelly MJ, Kay LE, Forman-Kay J, Serrano L. Similarities between the spectrin SH3 domain denatured state and its folding transition state. J Mol Biol 2000; 297:1217-29. [PMID: 10764585 DOI: 10.1006/jmbi.2000.3618] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have expanded our description of the energy landscape for folding of the SH3 domain of chicken alpha-spectrin by a detailed structural characterization of its denatured state ensemble (DSE). This DSE is significantly populated under mildly acidic conditions in equilibrium with the folded state. Evidence from heteronuclear nuclear magnetic resonance (NMR) experiments on (2)H, (15)N-labeled protein suggests the presence of conformers whose residual structure bears some resemblence to the structure of the folding transition state of this protein. NMR analysis in a mutant with an engineered, non-native alpha-helical tendency shows a significant amount of local non-native structure in the mutant, while the overall characteristics of the DSE are unchanged. Comparison with recent theoretical predictions of SH3 domain folding reactions reveals an interesting correlation with the predicted early events. Based on these results and recent data from other systems, we propose that the DSE of a protein will resemble the intermediate or transition state of its nearest rate-limiting step, as a consequence of simple energetic and kinetic principles.
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Affiliation(s)
- T Kortemme
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, D-6917, Germany.
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16
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Abstract
The N-terminal SH3 domain of drk (drkN SH3) is unstable, existing in equilibrium between a folded state (Fexch) and an unfolded state (Uexch) under non-denaturing buffer conditions. Using a15N/2H-labeled sample, long range amide NOEs can be observed in the Uexchstate as a result of reduced relaxation, in some cases correlating protons over 40 residues apart. These long range NOEs disappear upon addition of 2 M guanidinium chloride, demonstrating that there are substantial differences between the Uexchand the guanidine denatured states. Calculations using the long range NOEs of the Uexchstate yield highly compact structures having non-native turns and a non-native buried tryptophan residue. These structures agree with experimental stopped-flow fluorescence data and analytical ultracentrifugation results. Since protein stability depends on the structural and dynamic properties of both the folded and unfolded states, this study provides insights into the stability of the drkN SH3 domain. These results provide the first strong NOE-based evidence for compact unfolded states of proteins and suggest that some unfolded states under physiological conditions have specific interactions leading to compact structures.
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Affiliation(s)
- Y K Mok
- and Department of Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
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17
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Wang A, Forman-Kay J, Luo Y, Luo M, Chow YH, Plumb J, Friesen JD, Tsui LC, Heng HH, Woolford JL, Hu J. Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome. Hum Mol Genet 1997; 6:2117-26. [PMID: 9328476 DOI: 10.1093/hmg/6.12.2117] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nuclear RNA splicing occurs in an RNA-protein complex, termed the spliceosome. U4/U6 snRNP is one of four essential small nuclear ribonucleoprotein (snRNP) particles (U1, U2, U5 and U4/U6) present in the spliceosome. U4/U6 snRNP contains two snRNAs (U4 and U6) and a number of proteins. We report here the identification and characterization of two human genes encoding U4/U6-associated splicing factors, Hprp3p and Hprp4p, respectively. Hprp3p is a 77 kDa protein, which is homologous to the Saccharomyces cerevisiae splicing factor Prp3p. Amino acid sequence analysis revealed two putative homologues in Caenorhabditis elegans and Schizosaccharomyces pombe. Polyclonal antibodies against Hprp3p were generated with His-tagged Hprp3p over-produced in Escherichia coli . This splicing factor can co-immunoprecipitate with U4, U6 and U5 snRNAs, suggesting that it is present in the U4/U6.U5 tri-snRNP. Hprp4p is a 58 kDa protein homologous to yeast splicing factor Prp4p. Like yeast Prp4p, the human homologue contains repeats homologous to the beta-subunit of G-proteins. These repeats are called WD repeats because there is a highly conserved dipeptide of tryptophan and aspartic acid present at the end of each repeat. The primary amino acid sequence homology between human Hprp4p and yeast Prp4p led to the discovery of two additional WD repeats in yeast Prp4p. Structural homology between these human and yeast splicing factors and the beta-subunit of G-proteins has been identified by sequence-similarity comparison and analysis of the protein folding by threading. Structural models of Hprp4p and Prp4p with a seven-blade beta-propeller topology have been generated based on the structure of beta-transducin. Hprp3p and Hprp4p have been shown to interact with each other and the first 100 amino acids of Hprp3p are not essential for this interaction. These experiments suggest that both Hprp3p and Hprp4p are components of human spliceosomes.
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Affiliation(s)
- A Wang
- Division of Respiratory Research, Hospital for Sick Children, University of Toronto, Toronto, Ontario M5G 1X8, Canada
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Li SC, Songyang Z, Vincent SJ, Zwahlen C, Wiley S, Cantley L, Kay LE, Forman-Kay J, Pawson T. High-affinity binding of the Drosophila Numb phosphotyrosine-binding domain to peptides containing a Gly-Pro-(p)Tyr motif. Proc Natl Acad Sci U S A 1997; 94:7204-9. [PMID: 9207069 PMCID: PMC23792 DOI: 10.1073/pnas.94.14.7204] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The phosphotyrosine-binding (PTB) domain is a recently identified protein module that has been characterized as binding to phosphopeptides containing an NPXpY motif (X = any amino acid). We describe here a novel peptide sequence recognized by the PTB domain from Drosophila Numb (dNumb), a protein involved in cell fate determination and asymmetric cell division during the development of the Drosophila nervous system. Using a Tyr-oriented peptide library to screen for ligands, the dNumb PTB domain was found to bind selectively to peptides containing a YIGPYphi motif (phi represents a hydrophobic residue). A synthetic peptide containing this sequence bound specifically to the isolated dNumb PTB domain in solution with a dissociation constant (Kd) of 5.78 +/- 0.74 microM. Interestingly, the affinity of this peptide for the dNumb PTB domain was increased (Kd = 1.41 +/- 0.10 microM) when the second tyrosine in the sequence was phosphorylated. Amino acid substitution studies of the phosphopeptide demonstrated that a core motif of sequence GP(p)Y is required for high-affinity binding to the dNumb PTB domain. Nuclear magnetic resonance experiments performed on isotopically labeled protein complexed with either Tyr- or pTyr-containing peptides suggest that the same set of amino acids in the dNumb PTB domain is involved in binding both phosphorylated and nonphosphorylated forms of the peptide. The in vitro selectivity of the dNumb PTB domain is therefore markedly different from those of the Shc and IRS-1 PTB domains, in that it interacts preferentially with a GP(p)Y motif, rather than NPXpY, and does not absolutely require ligand phosphorylation for binding. Our results suggest that the PTB domain is a versatile protein module, capable of exhibiting varied binding specificities.
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Affiliation(s)
- S C Li
- Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
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Gasmi G, Singer A, Forman-Kay J, Sarkar B. NMR structure of neuromedin C, a neurotransmitter with an amino terminal CuII-, NiII-binding (ATCUN) motif. J Pept Res 1997; 49:500-9. [PMID: 9266477 DOI: 10.1111/j.1399-3011.1997.tb01157.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The structure of neuromedin C, a 10-residue bombesin-like neuropeptide with the sequence Gly-Asn-His-Trp-Ala-Val-Gly-His-Leu-Met-NH2, has been investigated. Like human serum albumin, neuromedin C contains the amino-terminal CuII-, NiII-binding (ATCUN) motif which has high affinity for CuII and NiII. The solution structure of the NiII-peptide complex has been calculated based on 2D ROESY data obtained at 25 degrees C, using a hybrid distance geometry-simulated annealing approach. Comparison of 1H, 13C and 15N chemical shifts and ROESY data in the presence and absence of NiII demonstrates that the metal binds at the N-terminus of the peptide, leading to a conformational change. The metal complex adopts a conformation comprising two connected turns including residues 1Gly to 3His and 5Ala to 8His. The first turn corresponds to the NiII coordination ligands in a square planar conformation, and the second reflects the interaction between 4Trp and 8His. The results may have important physiological implications in the phenomenon of neurotransmission.
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Affiliation(s)
- G Gasmi
- Department of Biochemistry Research, Hospital for Sick Children, Toronto, Ontario, Canada
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Li SC, Lai KM, Gish GD, Parris WE, van der Geer P, Forman-Kay J, Pawson T. Characterization of the phosphotyrosine-binding domain of the Drosophila Shc protein. J Biol Chem 1996; 271:31855-62. [PMID: 8943228 DOI: 10.1074/jbc.271.50.31855] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The phosphotyrosine-binding (PTB) domain of Drosophila Shc (dShc) binds in vitro to phosphopeptides containing the sequence motif NPXpY, and physically associates with the activated Drosophila epidermal growth factor receptor homologue (DER) in vivo. The structural elements, specificity and binding kinetics of the dShc PTB domain have now been characterized. The dShc PTB domain appeared similar to the insulin-like receptor substrate-1 PTB domain in secondary structure as suggested by Fourier transform infrared spectroscopy. Surface plasmon resonance measurements indicated that the dShc PTB domain bound with high affinity to phosphopeptides (Der) derived from the Tyr1228 site of the DER receptor. The kinetics of the dShc PTB domain-Der phosphopeptide interaction differed from those of a typical SH2 domain-ligand interaction, in that the PTB domain displayed slower on/off rates. Competition binding assays using truncated versions of the Der peptides revealed that high affinity binding to the dShc PTB domain requires, in addition to the NPXpY motif, the presence of hydrophobic residues at both positions -5 and -7 relative to phosphotyrosine. The dShc PTB domain showed a similar binding specificity to the human Shc (hShc) PTB domain, but subtle differences were noted; such that the hShc PTB domain bound preferentially to a phosphopeptide from the mammalian nerve growth factor receptor, whereas the dShc PTB domain bound preferentially to phosphopeptides from the Drosophila DER receptor. The invertebrate dShc PTB domain therefore possesses a binding specificity for tyrosine-phosphorylated peptides that is optimally suited for recognition of the activated DER receptor.
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Affiliation(s)
- S C Li
- Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.
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