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Singh RK, Chaurasiya AK, Kumar A. Ab initio modeling of human IRS1 protein to find novel target to dock with drug MH to mitigate T2DM diabetes by insulin signaling. 3 Biotech 2024; 14:108. [PMID: 38476643 PMCID: PMC10925585 DOI: 10.1007/s13205-024-03955-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 02/03/2024] [Indexed: 03/14/2024] Open
Abstract
IRS1 is a cytoplasmic adaptor protein that helps in cellular growth, glucose metabolism, proliferation, and differentiation. Highly disordered (insulin receptor substrate 1) IRS1 protein sequence (mol.wt- 131,590.97 da) has been used to develop model using ab initio modeling technique by I-Tassar tool and Discovery Studio/ DogSite Server to decipher a novel active site. The constructed protein model has been submitted with PMDB Id- PM0082210. GRAVY index of IRS1 model ( - 0.675) indicated surface protein-water interaction. Protparam tool instability index (75.22) demonstrated disorderedness combined with loops owing to prolines/glycines. After refinement, the Ramachandran plot showed that 88 percent of AAs were present in the allowed region and only 0.5% in the disallowed region. Novel IRS1 model protein has 10 α-helices, 22 β-sheets, 20 β-hairpins, 5 β-bulges, 47 strands, 105 β-turns, and 8 γ-turns. Docking of IRS1 with drug MH demonstrated interaction of Ser-70, Thr-18, and Pro-69 with C-H bonds; Gln-71, and Glu-113 with hydrogen bonds; while both Glu-114 and Glu-113 with salt-bridge connection. Permissible 1.0-1.5 Å range of RMSD fluctuation between 20 and 45 ns was obtained in simulation of IRS1 and IRS1-met complex confirmed that both complexes were stable during whole simulation process. RMSF result showed that except positions 57AA and 114AA, the binding of drug had no severe effects on the flexibility of the IRS1 and IRS1-met complex. The RoG value of compactness and rigidity showed little change in IRS1 protein. SASA value of IRS1 indicated non-significant fluctuation between IRS1 and drug MH means ligand (drug) and IRS1 receptor form stable structure. Hydrogen bond strength of IRS1 and IRS1-met was 81.2 and 76.4, respectively, which suggested stable interaction.
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Affiliation(s)
- Ritika Kumari Singh
- School of Biotechnology, Institute of Science, BHU, Varanasi, Uttar Pradesh 221005 India
| | | | - Arvind Kumar
- School of Biotechnology, Institute of Science, BHU, Varanasi, Uttar Pradesh 221005 India
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Zhou K, Chen Q, Chen J, Liang D, Feng W, Liu M, Wang Q, Wang R, Ouyang Q, Quan C, Chen S. Spatiotemporal regulation of insulin signaling by liquid–liquid phase separation. Cell Discov 2022; 8:64. [PMID: 35790738 PMCID: PMC9256590 DOI: 10.1038/s41421-022-00430-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/04/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractInsulin signals through its receptor to recruit insulin receptor substrates (IRS) and phosphatidylinositol 3-kinase (PI3K) to the plasma membrane for production of phosphatidylinositol-3,4,5-trisphosphate (PIP3) from phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2], which consequently activates protein kinase B (PKB). How insulin signals transduce from the plasma membrane into the cytoplasm is not clearly understood. Here we show that liquid–liquid phase separation (LLPS) plays a critical role in spatiotemporal control of insulin signaling through regulating multiple components including IRS1. Both protein concentration and insulin stimulation can drive the formation of intracellular IRS1 condensates through LLPS. Components including PI(4,5)P2, p85-PI3K and PDK1 are constitutively present in IRS1 condensates whereas production of PIP3 and recruitment of PKB in them are induced by insulin. Thus, IRS1 condensates function as intracellular signal hubs to mediate insulin signaling, whose formation is impaired in insulin resistant cells. Collectively, these data reveal an important function of LLPS in spatiotemporal control of insulin signaling.
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Padarti A, Abou-Fadel J, Zhang J. Resurgence of phosphotyrosine binding domains: Structural and functional properties essential for understanding disease pathogenesis. Biochim Biophys Acta Gen Subj 2021; 1865:129977. [PMID: 34391832 DOI: 10.1016/j.bbagen.2021.129977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Phosphotyrosine Binding (PTB) Domains, usually found on scaffold proteins, are pervasive in many cellular signaling pathways. These domains are the second-largest family of phosphotyrosine recognition domains and since their initial discovery, dozens of PTB domains have been structurally determined. SCOPE OF REVIEW Due to its signature sequence flexibility, PTB domains can bind to a large variety of ligands including phospholipids. PTB peptide binding is divided into classical binding (canonical NPXY motifs) and non-classical binding (all other motifs). The first atypical PTB domain was discovered in cerebral cavernous malformation 2 (CCM2) protein, while only one third in size of the typical PTB domain, it remains functionally equivalent. MAJOR CONCLUSIONS PTB domains are involved in numerous signaling processes including embryogenesis, neurogenesis, and angiogenesis, while dysfunction is linked to major disorders including diabetes, hypercholesterolemia, Alzheimer's disease, and strokes. PTB domains may also be essential in infectious processes, currently responsible for the global pandemic in which viral cellular entry is suspected to be mediated through PTB and NPXY interactions. GENERAL SIGNIFICANCE We summarize the structural and functional updates in the PTB domain over the last 20 years in hopes of resurging interest and further analyzing the importance of this versatile domain.
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Affiliation(s)
- Akhil Padarti
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, 5001 El Paso Drive, El Paso, TX 79905, USA
| | - Johnathan Abou-Fadel
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, 5001 El Paso Drive, El Paso, TX 79905, USA
| | - Jun Zhang
- Department of Molecular and Translational Medicine (MTM), Texas Tech University Health Science Center El Paso, 5001 El Paso Drive, El Paso, TX 79905, USA.
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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The AP-1 complex regulates intracellular localization of insulin receptor substrate 1, which is required for insulin-like growth factor I-dependent cell proliferation. Mol Cell Biol 2013; 33:1991-2003. [PMID: 23478262 DOI: 10.1128/mcb.01394-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The activation of the insulin/insulin-like growth factor I (IGF-I) receptor and the subsequent tyrosine phosphorylation of insulin receptor substrates (IRSs) are key initial events in a variety of insulin/IGF bioactivities, including mitogenesis. It has been reported that IRS-1 associates with intracellular membrane compartments, and this localization is believed to be important for insulin/IGF signal transduction. However, the molecular mechanisms underlying IRS-1 localization remain unclear. Here we show that in L6 myoblasts, IRS-1 associates with μ1A of the ubiquitously expressed AP-1 complex, which packages cargo proteins into clathrin-coated vesicles derived from intracellular membranes. While wild-type IRS-1 was predominantly localized to vesicular structures, IRS-1 mutants lacking three YXXΦ motifs responsible for binding to μ1A were mislocalized to the mannose-6-phosphate receptor-positive structures, suggesting that AP-1-dependent transport to peripheral vesicles is inhibited in these mutants. Furthermore, deletion of AP-1 binding sites in IRS-1 impaired IGF-I-induced cell proliferation, accompanied by reduced tyrosine phosphorylation of IRS-1 and its association with phosphoinositide (PI) 3-kinase. These data demonstrate the importance of AP-1-dependent localization of IRS-1 in mediating IGF-I-stimulated signaling and maximum mitogenic response.
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Xu H, Xu G, Wang D, Zheng C, Wan L. Molecular cloning and tissue distribution of the phosphotyrosine interaction domain containing 1 (PID1) gene in Tianfu goat. Gene 2013; 515:71-7. [DOI: 10.1016/j.gene.2012.11.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/28/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
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Nagano M, Hoshino D, Koshiba S, Shuo T, Koshikawa N, Tomizawa T, Hayashi F, Tochio N, Harada T, Akizawa T, Watanabe S, Handa N, Shirouzu M, Kigawa T, Yokoyama S, Seiki M. ZF21 protein, a regulator of the disassembly of focal adhesions and cancer metastasis, contains a novel noncanonical pleckstrin homology domain. J Biol Chem 2011; 286:31598-609. [PMID: 21768110 PMCID: PMC3173091 DOI: 10.1074/jbc.m110.199430] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 07/09/2011] [Indexed: 12/20/2022] Open
Abstract
Directional migration of adherent cells on an extracellular matrix requires repeated formation and disassembly of focal adhesions (FAs). Directional migration of adherent cells We have identified ZF21 as a regulator of disassembly of FAs and cell migration, and increased expression of the gene has been linked to metastatic colon cancer. ZF21 is a member of a protein family characterized by the presence of the FYVE domain, which is conserved among Fab1p, YOPB, Vps27p, and EEA1 proteins, and has been shown to mediate the binding of such proteins to phosphoinositides in the lipid layers of cell membranes. ZF21 binds multiple factors that promote disassembly of FAs such as FAK, β-tubulin, m-calpain, and SHP-2. ZF21 does not contain any other known protein motifs other than the FYVE domain, but a region of the protein C-terminal to the FYVE domain is sufficient to mediate binding to β-tubulin. In this study, we demonstrate that the C-terminal region is important for the ability of ZF21 to induce disassembly of FAs and cell migration, and to promote an early step of experimental metastasis to the lung in mice. In light of the importance of the C-terminal region, we analyzed its ternary structure using NMR spectroscopy. We demonstrate that this region exhibits a structure similar to that of a canonical pleckstrin homology domain, but that it lacks a positively charged interface to bind phosphatidylinositol phosphate. Thus, ZF21 contains a novel noncanonical PH-like domain that is a possible target to develop a therapeutic strategy to treat metastatic cancer.
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Affiliation(s)
- Makoto Nagano
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
- the Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotogecho, Hirakata Osaka, 573-0101
| | - Daisuke Hoshino
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Seizo Koshiba
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takuya Shuo
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Naohiko Koshikawa
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Tadashi Tomizawa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Fumiaki Hayashi
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Naoya Tochio
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takushi Harada
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Toshifumi Akizawa
- the Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotogecho, Hirakata Osaka, 573-0101
| | - Satoru Watanabe
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Noriko Handa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Mikako Shirouzu
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takanori Kigawa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuda-cho, Midori-ku, Yokohama 226-8502, and
| | - Shigeyuki Yokoyama
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motoharu Seiki
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
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Gao J, Takeuchi H, Zhang Z, Fujii M, Kanematsu T, Hirata M. Binding of phospholipase C-related but catalytically inactive protein to phosphatidylinositol 4,5-bisphosphate via the PH domain. Cell Signal 2009; 21:1180-6. [DOI: 10.1016/j.cellsig.2009.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 03/09/2009] [Indexed: 10/21/2022]
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Sun XJ, Liu F. Phosphorylation of IRS proteins Yin-Yang regulation of insulin signaling. VITAMINS AND HORMONES 2009; 80:351-87. [PMID: 19251044 DOI: 10.1016/s0083-6729(08)00613-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Growing evidence reveals that insulin signal pathway is not static, but is rather a dynamic, flexible, and fed in by negative (Yin) and positive (Yang) regulation in response to environmental changes. Normal insulin response reflects the balance between Yin and Yang regulation acting upon insulin signaling pathway. Conceivably, imbalance between the Yin and Yang results in abnormal insulin sensitivity such as insulin resistance. IRS-proteins are insulin receptor substrates that mediate insulin signaling via multiple tyrosyl phosphorylations. However, they are also substrates for many serine/threonine kinases downstream of other signaling network and become serine phosphorylated in response to various conditions such as inflammation, stress and over nutrients. The serine phosphorylation of IRS-proteins alters the capacities of IRS-proteins to be phosphorylated on tyrosyl, therefore, able to mediate insulin signaling. The unique structure of IRS-proteins render them idea molecules to fulfill the task to sense the environmental cues and integrate them into insulin sensitivity through serine/threonine phosphorylation. This review intends to summarize the role of IRS-proteins in insulin signaling with focuses on the role of Yin and Yang regulation of insulin signaling pathway. Understanding the dynamic of these complicated regulation net work not only provide us a complete picture of what happens in the normal conditions, but also pathaphysiological conditions such as obesity and insulin resistance.
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Affiliation(s)
- Xiao Jian Sun
- Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
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Jarymowycz VA, Stone MJ. Remote changes in the dynamics of the phosphotyrosine-binding domain of insulin receptor substrate-1 induced by phosphopeptide binding. Biochemistry 2009; 47:13371-82. [PMID: 19053277 DOI: 10.1021/bi801096b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein structures consist of cooperative networks of interactions that can extend substantial distances across the protein structure and have significant consequences for stability and function. To characterize such interaction networks within the phosphotyrosine-binding domain of insulin receptor substrate-1 (IRS-PTB), we have used NMR relaxation to determine the dynamics of backbone amide groups, side chain methyl groups, and tryptophan side chain indole groups in IRS-PTB, both in the absence and in the presence of a bound phosphotyrosine-containing peptide. Although there are minimal differences between the structures of apo and peptide-bound forms, primarily localized close to the peptide binding site, we observe significant changes in dynamics for residues located remotely from the binding site. These residues are clustered together and appear to constitute a network of interactions that is coupled to the peptide binding site through intervening residues.
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Affiliation(s)
- Virginia A Jarymowycz
- Department of Chemistry and Interdisciplinary Biochemistry Program, Indiana University, Bloomington, Indiana 47405-0001, USA
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Leone M, Yu EC, Liddington RC, Pasquale EB, Pellecchia M. The PTB domain of tensin: NMR solution structure and phosphoinositides binding studies. Biopolymers 2008; 89:86-92. [DOI: 10.1002/bip.20862] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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PKCdelta-mediated IRS-1 Ser24 phosphorylation negatively regulates IRS-1 function. Biochem Biophys Res Commun 2006; 349:976-86. [PMID: 16970908 DOI: 10.1016/j.bbrc.2006.08.158] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 08/19/2006] [Indexed: 11/28/2022]
Abstract
The IRS-1 PH and PTB domains are essential for insulin-stimulated IRS-1 Tyr phosphorylation and insulin signaling, while Ser/Thr phosphorylation of IRS-1 disrupts these signaling events. To investigate consensus PKC phosphorylation sites in the PH-PTB domains of human IRS-1, we changed Ser24, Ser58, and Thr191 to Ala (3A) or Glu (3E), to block or mimic phosphorylation, respectively. The 3A mutant abrogated the inhibitory effect of PKCdelta on insulin-stimulated IRS-1 Tyr phosphorylation, while reductions in insulin-stimulated IRS-1 Tyr phosphorylation, cellular proliferation, and Akt activation were observed with the 3E mutant. When single Glu mutants were tested, the Ser24 to Glu mutant had the greatest inhibitory effect on insulin-stimulated IRS-1 Tyr phosphorylation. PKCdelta-mediated IRS-1 Ser24 phosphorylation was confirmed in cells with PKCdelta catalytic domain mutants and by an RNAi method. Mechanistic studies revealed that IRS-1 with Ala and Glu point mutations at Ser24 impaired phosphatidylinositol-4,5-bisphosphate binding. In summary, our data are consistent with the hypothesis that Ser24 is a negative regulatory phosphorylation site in IRS-1.
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Uhlik MT, Temple B, Bencharit S, Kimple AJ, Siderovski DP, Johnson GL. Structural and evolutionary division of phosphotyrosine binding (PTB) domains. J Mol Biol 2005; 345:1-20. [PMID: 15567406 DOI: 10.1016/j.jmb.2004.10.038] [Citation(s) in RCA: 205] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 10/13/2004] [Accepted: 10/13/2004] [Indexed: 11/21/2022]
Abstract
Proteins encoding phosphotyrosine binding (PTB) domains function as adaptors or scaffolds to organize the signaling complexes involved in wide-ranging physiological processes including neural development, immunity, tissue homeostasis and cell growth. There are more than 200 proteins in eukaryotes and nearly 60 human proteins having PTB domains. Six PTB domain encoded proteins have been found to have mutations that contribute to inherited human diseases including familial stroke, hypercholesteremia, coronary artery disease, Alzheimer's disease and diabetes, demonstrating the importance of PTB scaffold proteins in organizing critical signaling complexes. PTB domains bind both peptides and headgroups of phosphatidylinositides, utilizing two distinct binding motifs to mediate spatial organization and localization within cells. The structure of PTB domains confers specificity for binding peptides having a NPXY motif with differing requirements for phosphorylation of the tyrosine within this recognition sequence. In this review, we use structural, evolutionary and functional analysis to divide PTB domains into three groups represented by phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like and phosphotyrosine-independent Dab-like PTBs, with the Dab-like PTB domains representing nearly 75% of proteins encoding PTB domains. In addition, we further define the binding characteristics of the cognate ligands for each group of PTB domains. The signaling complexes organized by PTB domain encoded proteins are largely unknown and represents an important challenge in systems biology for the future.
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Affiliation(s)
- Mark T Uhlik
- Department of Pharmacology and University of North Carolina School of Medicine, 1108 Mary Ellen Jones Building, Campus Box 7365, Chapel Hill, NC 27599-7365, USA
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Bedirian A, Baldwin C, Abe JI, Takano T, Lemay S. Pleckstrin Homology and Phosphotyrosine-binding Domain-dependent Membrane Association and Tyrosine Phosphorylation of Dok-4, an Inhibitory Adapter Molecule Expressed in Epithelial Cells. J Biol Chem 2004; 279:19335-49. [PMID: 14963042 DOI: 10.1074/jbc.m310689200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dok-like adapter molecules represent an expanding family of pleckstrin homology (PH) and phosphotyrosine-binding (PTB) domain-containing tyrosine kinase substrates with negative regulatory functions in hematopoietic cell signaling. In a search for nonhematopoietic counterparts to Dok molecules, we identified and characterized Dok-4, a recently cloned member of the family. dok-4 mRNA was strongly expressed in nonhematopoietic organs, particularly the intestine, kidney, and lung, whereas both mRNA and protein were expressed at high levels in cells of epithelial origin. In Caco-2 human colon cancer cells, endogenous Dok-4 underwent tyrosine phosphorylation in response to pervanadate stimulation. In transfected COS cells, Dok-4 was a substrate for the cytosolic tyrosine kinases Src and Fyn as well as for Jak2. Dok-4 could also be phosphorylated by the receptor tyrosine kinase Ret but not by platelet-derived growth factor receptor-beta or IGF-IR. In both mammalian cells and yeast, Dok-4 was constitutively localized at the membrane in a manner that required both its PH and PTB domains. The PH and PTB domains of Dok-4 were also required for tyrosine phosphorylation of Dok-4 by Fyn and Ret. Finally, wild type Dok-4 strongly inhibited activation of Elk-1 induced by either Ret or Fyn. The attenuation of this inhibitory effect by deletion of the PH domain and its restoration by the addition of a myristoylation signal suggested an important role for constitutive membrane localization of Dok-4. In summary, Dok-4 is a constitutively membrane-localized adapter molecule that may function as an inhibitor of tyrosine kinase signaling in epithelial cells.
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Affiliation(s)
- Arda Bedirian
- Department of Medicine, Division of Nephrology, McGill University Health Centre, Montreal, Quebec H3A 2B4, Canada
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Schlessinger J, Lemmon MA. SH2 and PTB domains in tyrosine kinase signaling. SCIENCE'S STKE : SIGNAL TRANSDUCTION KNOWLEDGE ENVIRONMENT 2003; 2003:RE12. [PMID: 12865499 DOI: 10.1126/stke.2003.191.re12] [Citation(s) in RCA: 171] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Intracellular signaling pathways that involve protein tyrosine kinases (PTKs) are critical for the control of most cellular processes. Dysfunctions in PTKs, or in the signaling pathways that they regulate, result in a variety of diseases such as cancer, diabetes, immune deficiency, and many others. SH2 (Src homology region 2) and PTB (phosphotyrosine-binding) domains are small protein modules that mediate protein-protein interactions involved in many signal transduction pathways. Both domains were initially identified as modules that recognize phosphorylated tyrosines in receptor tyrosine kinases and other signaling proteins. Subsequent studies have shown that, while binding of SH2 domains to their target proteins is strictly regulated by tyrosine phosphorylation, most PTB domains actually bind to their (nonphosphorylated) targets constitutively. The functions of SH2 and PTB domains include targeting of their host proteins to different cellular compartments, assembly of key components of signaling pathways in response to extracellular signals, and the control of autoinhibition, activation and dimerization of their host proteins. The information flow from the cell surface to different cellular compartments to regulate the cell cycle, cell shape and movement, cell proliferation, differentiation and cell survival are all controlled in part by SH2 and PTB domains that can recognize phosphotyrosine or particular amino acid sequence motifs in a wide variety of target molecules.
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Affiliation(s)
- Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Ago T, Kuribayashi F, Hiroaki H, Takeya R, Ito T, Kohda D, Sumimoto H. Phosphorylation of p47phox directs phox homology domain from SH3 domain toward phosphoinositides, leading to phagocyte NADPH oxidase activation. Proc Natl Acad Sci U S A 2003; 100:4474-9. [PMID: 12672956 PMCID: PMC153580 DOI: 10.1073/pnas.0735712100] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Indexed: 11/18/2022] Open
Abstract
Protein-phosphoinositide interaction participates in targeting proteins to membranes where they function correctly and is often modulated by phosphorylation of lipids. Here we show that protein phosphorylation of p47(phox), a cytoplasmic activator of the microbicidal phagocyte oxidase (phox), elicits interaction of p47(phox) with phosphoinositides. Although the isolated phox homology (PX) domain of p47(phox) can interact directly with phosphoinositides, the lipid-binding activity of this protein is normally suppressed by intramolecular interaction of the PX domain with the C-terminal Src homology 3 (SH3) domain, and hence the wild-type full-length p47(phox) is incapable of binding to the lipids. The W263R substitution in this SH3 domain, abrogating the interaction with the PX domain, leads to a binding of p47(phox) to phosphoinositides. The findings indicate that disruption of the intramolecular interaction renders the PX domain accessible to the lipids. This conformational change is likely induced by phosphorylation of p47(phox), because protein kinase C treatment of the wild-type p47(phox) but not of a mutant protein with the S303304328A substitution culminates in an interaction with phosphoinositides. Furthermore, although the wild-type p47(phox) translocates upon cell stimulation to membranes to activate the oxidase, neither the kinase-insensitive p47(phox) nor lipid-binding-defective proteins, one lacking the PX domain and the other carrying the R90K substitution in this domain, migrates. Thus the protein phosphorylation-driven conformational change of p47(phox) enables its PX domain to bind to phosphoinositides, the interaction of which plays a crucial role in recruitment of p47(phox) from the cytoplasm to membranes and subsequent activation of the phagocyte oxidase.
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Affiliation(s)
- Tetsuro Ago
- Medical Institute of Bioregulation, Kyushu University, and Department of Molecular and Structural Biology, Kyushu University Graduate School of Medicine, Fukuoka 812-8582, Japan
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18
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Mishra SK, Keyel PA, Hawryluk MJ, Agostinelli NR, Watkins SC, Traub LM. Disabled-2 exhibits the properties of a cargo-selective endocytic clathrin adaptor. EMBO J 2002; 21:4915-26. [PMID: 12234931 PMCID: PMC126284 DOI: 10.1093/emboj/cdf487] [Citation(s) in RCA: 259] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clathrin-coated pits at the cell surface select material for transportation into the cell interior. A major mode of cargo selection at the bud site is via the micro 2 subunit of the AP-2 adaptor complex, which recognizes tyrosine-based internalization signals. Other internalization motifs and signals, including phosphorylation and ubiquitylation, also tag certain proteins for incorporation into a coated vesicle, but the mechanism of selection is unclear. Disabled-2 (Dab2) recognizes the FXNPXY internalization motif in LDL-receptor family members via an N-terminal phosphotyrosine-binding (PTB) domain. Here, we show that in addition to binding AP-2, Dab2 also binds directly to phosphoinositides and to clathrin, assembling triskelia into regular polyhedral coats. The FXNPXY motif and phosphoinositides contact different regions of the PTB domain, but can stably anchor Dab2 to the membrane surface, while the distal AP-2 and clathrin-binding determinants regulate clathrin lattice assembly. We propose that Dab2 is a typical member of a growing family of cargo-specific adaptor proteins, including beta-arrestin, AP180, epsin, HIP1 and numb, which regulate clathrin-coat assembly at the plasma membrane by synchronizing cargo selection and lattice polymerization events.
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Affiliation(s)
- Sanjay K Mishra
- Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S325BST, Pittsburgh, PA 15261, USA
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19
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Jacobs AR, LeRoith D, Taylor SI. Insulin receptor substrate-1 pleckstrin homology and phosphotyrosine-binding domains are both involved in plasma membrane targeting. J Biol Chem 2001; 276:40795-802. [PMID: 11526109 DOI: 10.1074/jbc.m105194200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The localization of insulin receptor substrate (IRS) molecules may be responsible for the differential biological activities of insulin and other peptides such as platelet-derived growth factor. The subcellular localization of IRS-1 is controversial, with some reports suggesting association with the cytoskeleton and other studies reporting membrane localization. In this study, we used immunofluorescence microscopy to define the localization of IRS-1. In the basal state, recombinant IRS-1 was localized predominantly in the cytoplasm. In response to insulin, recombinant IRS-1 translocated to the plasma membrane. We have also studied the localization of green fluorescent protein (GFP) fusion proteins. Unlike native IRS-1, a fusion protein containing GFP plus full-length IRS-1 appeared to localize in inclusion bodies. In contrast, when GFP was fused to the N terminus of IRS-1 (i.e. the pleckstrin homology and phosphotyrosine-binding domains), this fusion protein was targeted to the plasma membrane. Mutations of phosphoinositide-binding sites in both the pleckstrin homology and phosphotyrosine-binding domains significantly reduced the ability of Myc-tagged IRS-1 to translocate to the plasma membrane following insulin stimulation. However, these mutations did not cause a statistically significant impairment of tyrosine phosphorylation in response to insulin. This raises the possibility that IRS-1 tyrosine phosphorylation may occur prior to plasma membrane translocation.
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Affiliation(s)
- A R Jacobs
- Diabetes Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-1758, USA
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20
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Ago T, Takeya R, Hiroaki H, Kuribayashi F, Ito T, Kohda D, Sumimoto H. The PX domain as a novel phosphoinositide- binding module. Biochem Biophys Res Commun 2001; 287:733-8. [PMID: 11563857 DOI: 10.1006/bbrc.2001.5629] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The phox (phagocyte oxidase) homology (PX) domain occurs in the mammalian phox proteins p40(phox) and p47(phox), the polarity establishment protein Bem1p in budding yeast, and a variety of proteins involved in membrane trafficking. Here we show that the PX domains of p40(phox) and p47(phox) directly bind to phosphoinositides: p40(phox) prefers Ptdlns(3)P, while p47(phox) does Ptdlns(4)P and Ptdlns(3,4)P(2). In addition, the Bem1p PX domain also interacts with Ptdlns(4)P. When the p40(phox) PX domain is expressed as a fusion to green fluorescent protein in HeLa cells, it exists at early endosomes where Ptdlns(3)P is enriched. Furthermore, a mutant p40(phox) PX carrying the substitution of Lys for Arg105 only weakly binds to phosphoinositides in vitro, and fails to locate to early endosomes. Thus the PX domain functions as a novel phosphoinositide-binding module and likely participates in targeting of proteins to membranes.
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Affiliation(s)
- T Ago
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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21
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Vainshtein I, Kovacina KS, Roth RA. The insulin receptor substrate (IRS)-1 pleckstrin homology domain functions in downstream signaling. J Biol Chem 2001; 276:8073-8. [PMID: 11145958 DOI: 10.1074/jbc.m008436200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pleckstrin homology (PH) domain of the insulin receptor substrate-1 (IRS-1) plays a role in directing this molecule to the insulin receptor, thereby regulating its tyrosine phosphorylation. In this work, the role of the PH domain in subsequent signaling was studied by constructing constitutively active forms of IRS-1 in which the inter-SH2 domain of the p85 subunit of phosphatidylinositol 3-kinase was fused to portions of the IRS-1 molecule. Chimeric molecules containing the PH domain were found to activate the downstream response of stimulating the Ser/Thr kinase Akt. A chimera containing point mutations in the PH domain that abolished the ability of this domain to bind phosphatidylinositol 4,5-bisphosphate prevented these molecules from activating Akt. These mutations also decreased by about 70% the amount of the constructs present in a particulate fraction of the cells. These results indicate that the PH domain of IRS-1, in addition to directing this protein to the receptor for tyrosine phosphorylation, functions in the ability of this molecule to stimulate subsequent responses. Thus, compromising the function of the PH domain, e.g. in insulin-resistant states, could decrease both the ability of IRS-1 to be tyrosine phosphorylated by the insulin receptor and to link to subsequent downstream targets.
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Affiliation(s)
- I Vainshtein
- Department of Molecular Pharmacology, Stanford University School of Medicine, Stanford, California 94305-5174, USA
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22
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Abstract
This review assesses the authenticity of inositol hexakisphosphate (InsP(6)) being a wide-ranging regulator of many important cellular functions. Against a background in which the possible importance of localized InsP(6) metabolism is discussed, there is the facile explanation that InsP(6) is merely an "inactive" precursor for the diphosphorylated inositol phosphates. Indeed, many of the proposed cellular functions of InsP(6) cannot sustain a challenge from the implementation of a rigorous set of criteria, which are designed to avoid experimental artefacts.
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Affiliation(s)
- S B Shears
- Inositol Signaling Section, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, 27709, Research Triangle Park, NC, USA.
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23
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Lemmon MA, Ferguson KM. Signal-dependent membrane targeting by pleckstrin homology (PH) domains. Biochem J 2000; 350 Pt 1:1-18. [PMID: 10926821 PMCID: PMC1221219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Pleckstrin homology (PH) domains are small protein modules of around 120 amino acids found in many proteins involved in cell signalling, cytoskeletal rearrangement and other processes. Although several different protein ligands have been proposed for PH domains, their only clearly demonstrated physiological function to date is to bind membrane phosphoinositides. The PH domain from phospholipase C-delta(1) binds specifically to PtdIns(4,5)P(2) and its headgroup, and has become a valuable tool for studying cellular PtdIns(4,5)P(2) functions. More recent developments have demonstrated that a subset of PH domains recognizes the products of agonist-stimulated phosphoinositide 3-kinases. Fusion of these PH domains to green fluorescent protein has allowed dramatic demonstrations of their independent ability to drive signal-dependent recruitment of their host proteins to the plasma membrane. We discuss the structural basis for this 3-phosphoinoistide recognition and the role that it plays in cellular signalling. PH domains that bind specifically to phosphoinositides comprise only a minority (perhaps 15%) of those known, raising questions as to the physiological role of the remaining 85% of PH domains. Most (if not all) PH domains bind weakly and non-specifically to phosphoinositides. Studies of dynamin-1 have indicated that oligomerization of its PH domain may be important in driving membrane association. We discuss the possibility that membrane targeting by PH domains with low affinity for phosphoinositides could be driven by alteration of their oligomeric state and thus the avidity of their membrane binding.
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Affiliation(s)
- M A Lemmon
- The Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar-Chance Laboratories, Philadelphia, PA 19104-6059, USA.
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24
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Takeuchi H, Oike M, Paterson HF, Allen V, Kanematsu T, Ito Y, Erneux C, Katan M, Hirata M. Inhibition of Ca(2+) signalling by p130, a phospholipase-C-related catalytically inactive protein: critical role of the p130 pleckstrin homology domain. Biochem J 2000; 349:357-68. [PMID: 10861248 PMCID: PMC1221157 DOI: 10.1042/0264-6021:3490357] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
p130 was originally identified as an Ins(1,4,5)P(3)-binding protein similar to phospholipase C-delta but lacking any phospholipase activity. In the present study we have further analysed the interactions of p130 with inositol compounds in vitro. To determine which of the potential ligands interacts with p130 in cells, we performed an analysis of the cellular localization of this protein, the isolation of a protein-ligand complex from cell lysates and studied the effects of p130 on Ins(1,4,5)P(3)-mediated Ca(2+) signalling by using permeabilized and transiently or stably transfected COS-1 cells (COS-1(p130)). In vitro, p130 bound Ins(1,4,5)P(3) with a higher affinity than that for phosphoinositides. When the protein was isolated from COS-1(p130) cells by immunoprecipitation, it was found to be associated with Ins(1,4,5)P(3). Localization studies demonstrated the presence of the full-length p130 in the cytoplasm of living cells, not at the plasma membrane. In cell-based assays, p130 had an inhibitory effect on Ca(2+) signalling. When fura-2-loaded COS-1(p130) cells were stimulated with bradykinin, epidermal growth factor or ATP, it was found that the agonist-induced increase in free Ca(2+) concentration, observed in control cells, was inhibited in COS-1(p130). This inhibition was not accompanied by the decreased production of Ins(1,4,5)P(3); the intact p130 pleckstrin homology domain, known to be the ligand-binding site in vitro, was required for this effect in cells. These results suggest that Ins(1,4,5)P(3) could be the main p130 ligand in cells and that this binding has the potential to inhibit Ins(1,4,5)P(3)-mediated Ca(2+) signalling.
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Affiliation(s)
- H Takeuchi
- Department of Biochemistry, Faculty of Dentistry, Kyushu University and Kyushu University Station for Collaborative Research, Fukuoka 812-8582, Japan
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25
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Stricker R, Adelt S, Vogel G, Reiser G. Translocation between membranes and cytosol of p42IP4, a specific inositol 1,3,4,5-tetrakisphosphate/phosphatidylinositol 3,4, 5-trisphosphate-receptor protein from brain, is induced by inositol 1,3,4,5-tetrakisphosphate and regulated by a membrane-associated 5-phosphatase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:815-24. [PMID: 10504414 DOI: 10.1046/j.1432-1327.1999.00795.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The highly conserved 42-kDa protein, p42IP4 was identified recently from porcine brain. It has also been identified similarly in bovine, rat and human brain as a protein with two pleckstrin homology domains that binds Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3 with high affinity and selectivity. The brain-specific p42IP4 occurs both as membrane-associated and cytosolic protein. Here, we investigate whether p42IP4 can be translocated from membranes by ligand interaction. p42IP4 is released from cerebellar membranes by incubation with Ins(1,3,4,5)P4. This dissociation is concentration-dependent (> 100 nM), occurs within a few minutes and and is ligand-specific. p42IP4 specifically associates with PtdIns(3, 4,5)P3-containing lipid vesicles and can dissociate from these vesicles by addition of Ins(1,3,4,5)P4. p42IP4 is only transiently translocated from the membranes as Ins(1,3,4,5)P4 can be degraded by a membrane-associated 5-phosphatase to Ins(1,3,4)P3. Then, p42IP4 re-binds to the membranes from which it can be re-released by re-addition of Ins(1,3,4,5)P4. Thus, Ins(1,3,4,5)P4 specifically induces the dissociation from membranes of a PtdIns(3,4,5)P3 binding protein that can reversibly re-associate with the membranes. Quantitative analysis of the inositol phosphates in rat brain tissue revealed a concentration of Ins(1,3,4,5)P4 comparable to that required for p42IP4 translocation. Thus, in vivo p42IP4 might interact with membranes in a ligand-controlled manner and be involved in physiological processes induced by the two second messengers Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3.
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Affiliation(s)
- R Stricker
- Institut für Neurobiochemie, Otto-von-Guericke-Universität Magdeburg, Germany
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26
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Yamamoto T, Takeuchi H, Kanematsu T, Allen V, Yagisawa H, Kikkawa U, Watanabe Y, Nakasima A, Katan M, Hirata M. Involvement of EF hand motifs in the Ca(2+)-dependent binding of the pleckstrin homology domain to phosphoinositides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:481-90. [PMID: 10491207 DOI: 10.1046/j.1432-1327.1999.00786.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The pleckstrin homology (PH) domains of phospholipase C (PLC)-delta1 and a related catalytically inactive protein, p130, both bind inositol phosphates and inositol lipids. The binding to phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] by PLC-delta1 is proposed to be the critical interaction required for membrane localization to where the substrate resides; it is also required for the Ca(2+)-dependent activation of PLC-delta1 observed in the permeabilized cells. In the proximity of the PH domain, both PLC-delta1 and p130 possess the EF-hand domain, containing classical motifs implicated in calcium binding. Therefore, in the present study we examined whether the binding of the PH domain to PtdIns(4,5)P2 is regulated by changes in free Ca2+ concentration within the physiological range. A Ca2+ dependent increase in the binding to PtdIns(4,5)P2 was observed with a full-length PLC-delta1, while the isolated PH domain did not show any Ca2+ dependence. However, the connection of the EF-hand motifs to the PH domain restored the Ca2+ dependent increase in binding, even in the absence of the C2 domain. The p130 protein showed similar properties to PLC-delta1, and the EF-hand motifs were again required for the PH domain to exhibit a Ca2+ dependent increase in the binding to PtdIns(4,5)P2. The isolated PH domains from several other proteins which have been demonstrated to bind PtdIns(4,5)P2 showed no Ca2+ dependent enhancement of binding. However, when present within a chimera also containing PLC-delta1 EF-hand motifs, the Ca2+ dependent binding was again observed. These results suggest that the binding of Ca2+ to the EF-hand motifs can modulate binding to PtdIns(4,5)P2 mediated by the PH domain.
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Affiliation(s)
- T Yamamoto
- Department of Biochemistry, Faculty of Dentistry, Kyushu University, Fukuoka, Japan
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27
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Abstract
The phosphotyrosine-binding domain is a recently described protein-protein interaction domain which, despite its name, is involved in both phosphotyrosine-dependent and -independent interactions. Proteins with this domain are involved in diverse cellular functions, ranging from receptor signaling to protein targeting.
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28
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Liu L, Makowske M. Phosphotyrosine protein of molecular mass 30 kDa binds specifically to the positively charged region of the pleckstrin N-terminal pleckstrin homology domain. Biochem J 1999; 342 ( Pt 2):423-30. [PMID: 10455030 PMCID: PMC1220480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
It has been proposed that phosphoinositides and inositol phosphates serve as general ligands for members of the structurally related pleckstrin homology (PH) domain family. The N-terminal PH domain of pleckstrin (N-PH), in contrast with other PH domains, does not bind to any of these ligands with the high affinity expected for a physiological interaction. To examine whether N-PH might instead mediate protein-protein interaction, a fusion protein with glutathione S-transferase (GST) expressing N-PH (GST-N-PH) was used to screen [(35)S]methionine metabolically labelled HL-60 and Bac1. 2F5 cell lysates for potential binding partners. A 30 kDa binding protein was identified in both cell lines. Binding to N-PH demonstrated specificity, because binding was approx. 10-fold higher than when an equimolar amount of pleckstrin C-terminal PH domain (GST-C-PH) was used as probe. The 30 kDa protein could also be metabolically labelled with [(32)P]P(i) and proved to be a tyrosine-phosphorylated protein. Binding to N-PH could be specifically inhibited with phosphotyrosine but not with phosphothreonine; the inhibition was concentration-dependent. Site-directed mutagenesis indicated that a positively charged region previously identified as the phosphoinositide-binding site in N-PH and other PH domains, rather than a putative phosphotyrosine-binding region previously identified in structurally similar phosphotyrosine-binding (PTB) domains, served as the binding site. These results suggest that the positively charged region of N-PH has the potential to interact with a protein ligand that contains phosphotyrosine.
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Affiliation(s)
- L Liu
- Department of Biochemistry, State University of New York Health Science Center at Brooklyn, 450 Clarkson, Brooklyn, NY 11203, USA
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29
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Baron CB, Tolan DR, Choi KH, Coburn RF. Aldolase A Ins(1,4,5)P3-binding domains as determined by site-directed mutagenesis. Biochem J 1999; 341 ( Pt 3):805-12. [PMID: 10417347 PMCID: PMC1220421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
We substituted neutral amino acids for some positively charged residues (R42, K107, K146, R148 and K229) that line the active site of aldolase A in an effort to determine binding sites for inositol 1, 4,5-trisphosphate. In addition, D33 (involved in carbon-carbon bond cleavage) was mutated. K229A and D33S aldolases showed almost no catalytic activity, but Ins(1,4,5)P(3) binding was similar to that determined with the use of wild-type aldolase A. R42A, K107A, K146R and R148A had markedly decreased affinities for Ins(1,4,5)P(3) binding, increased EC(50) values for Fru(1,6)P(2)-evoked release of bound Ins(1,4,5)P(3) and increased K(i) values for Ins(1,4, 5)P(3)-evoked inhibition of aldolase activity. K146Q (positive charge removal) had essentially no catalytic activity and could not bind Ins(1,4,5)P(3). Computer-simulated docking of Ins(1,4,5)P(3) in the aldolase A structure was consistent with electrostatic binding of Ins(1,4,5)P(3) to K107, K146, R148, R42, R303 and backbone nitrogens, as has been reported for Fru(1,6)P(2) binding. Results indicate that Ins(1,4,5)P(3) binding occurs at the active site and is not dependent on having a catalytically active enzyme; they also suggest that there is competition between Ins(1,4,5)P(3) and Fru(1, 6)P(2) for binding. Although Ins(1,4,5)P(3) binding to aldolase involved electrostatic interactions, the aldolase A Ins(1,4, 5)P(3)-binding domain did not show other similarities to pleckstrin homology domains or phosphotyrosine-binding domains known to bind Ins(1,4,5)P(3) in other proteins.
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Affiliation(s)
- C B Baron
- Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6085, USA.
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30
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Dhe-Paganon S, Ottinger EA, Nolte RT, Eck MJ, Shoelson SE. Crystal structure of the pleckstrin homology-phosphotyrosine binding (PH-PTB) targeting region of insulin receptor substrate 1. Proc Natl Acad Sci U S A 1999; 96:8378-83. [PMID: 10411883 PMCID: PMC17524 DOI: 10.1073/pnas.96.15.8378] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have determined the crystal structure at 2.3-A resolution of an amino-terminal segment of human insulin receptor substrate 1 that encompasses its pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains. Both domains adopt the canonical seven-stranded beta-sandwich PH domain fold. The domains are closely associated, with a 720-A(2) contact surface buried between them that appears to be stabilized by ionic, hydrophobic, and hydrogen bonding interactions. The nonconserved 46-residue linker between the domains is disordered. The PTB domain peptide binding site is fully exposed on the molecular surface, as is a large cationic patch at the base of the PH domain that is a likely binding site for the head groups of phosphatidylinositol phosphates. Binding assays confirm that phosphatidylinositol phosphates bind the PH domain, but not the PTB domain. Ligand binding to the PH domain does not alter PTB domain interactions, and vice versa. The structural and accompanying functional data illustrate how the two binding domains might act cooperatively to effectively increase local insulin receptor substrate 1 concentration at the membrane and transiently fix the receptor and substrate, to allow multiple phosphorylation reactions to occur during each union.
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Affiliation(s)
- S Dhe-Paganon
- Joslin Diabetes Center and the Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
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31
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Aikawa Y, Kuraoka A, Kondo H, Kawabuchi M, Watanabe T. Involvement of PITPnm, a mammalian homologue of Drosophila rdgB, in phosphoinositide synthesis on Golgi membranes. J Biol Chem 1999; 274:20569-77. [PMID: 10400687 DOI: 10.1074/jbc.274.29.20569] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphatidylinositol transfer protein (PITP) is involved in phospholipase C-mediated signaling and membrane trafficking. We previously reported cloning and characterization of a gene encoding for membrane-bound PITP, named PITPnm, that is a mammalian homologue of the Drosophila retinal degeneration B (rdgB) gene (Aikawa, Y., Hara, H., and Watanabe, T. (1997) Biochem. Biophys. Res. Commun. 236, 559-564). Here we report the subcellular localization of PITPnm protein and provide evidence for its involvement in phosphatidylinositol 4-phosphate (PtdIns 4-P) synthesis. PITPnm is an integral membrane protein that largely localized in close association with membranes of Golgi vacuoles and the endoplasmic reticulum (ER). The amino terminus region of PITPnm was exposed to cytoplasmic side. Interaction with various phosphoinositides was observed in the amino terminus region spanning from 196 amino acids to 257 amino acids of PITPnm. At the amino terminus regions of 1-372 amino acids, PITPnm formed a complex with type III PtdIns 4-kinase. The transmembrane and carboxyl-terminal portions (residues 418-1242) functioned to retain the PITPnm in the Golgi vacuole. These results suggest that PITPnm plays a role in phosphoinositide synthesis on the Golgi vacuoles and possibly in the PtdIns signaling pathway in mammalian cells.
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Affiliation(s)
- Y Aikawa
- Department of Molecular Immunology, Medical Institute of Bioregulation, Fukuoka City, Fukuoka 812-8582, Japan
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32
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Hinchliffe KA, Ciruela A, Irvine RF. PIPkins1, their substrates and their products: new functions for old enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1436:87-104. [PMID: 9838059 DOI: 10.1016/s0005-2760(98)00140-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
The phosphatidylinositolphosphate kinases (PIPkins) are a unique family of enzymes that catalyse the production of phosphorylated inositol lipids. Recent advances have revealed that, due to their ability to utilise a number of different lipid substrates (at least in vitro), this family is potentially able to generate several distinct, physiologically important inositol lipids. Despite their importance, however, our understanding of the regulation of the PIPkins and of their physiological role in cellular signalling and regulation is still poor. Here we describe in turn the diverse physiological functions of the known substrates and major products of the PIPkins. We then examine what is known about the members of the PIPkin family themselves, and their characteristics and regulation.
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Affiliation(s)
- K A Hinchliffe
- University of Cambridge, Department of Pharmacology, Tennis Court Road, Cambridge CB2 1QJ, UK.
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