1
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Pellegrini E, Signor L, Singh S, Boeri Erba E, Cusack S. Structures of the inactive and active states of RIP2 kinase inform on the mechanism of activation. PLoS One 2017; 12:e0177161. [PMID: 28545134 PMCID: PMC5436651 DOI: 10.1371/journal.pone.0177161] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
Innate immune receptors NOD1 and NOD2 are activated by bacterial peptidoglycans leading to recruitment of adaptor kinase RIP2, which, upon phosphorylation and ubiquitination, becomes a scaffold for downstream effectors. The kinase domain (RIP2K) is a pharmaceutical target for inflammatory diseases caused by aberrant NOD2-RIP2 signalling. Although structures of active RIP2K in complex with inhibitors have been reported, the mechanism of RIP2K activation remains to be elucidated. Here we analyse RIP2K activation by combining crystal structures of the active and inactive states with mass spectrometric characterization of their phosphorylation profiles. The active state has Helix αC inwardly displaced and the phosphorylated Activation Segment (AS) disordered, whilst in the inactive state Helix αC is outwardly displaced and packed against the helical, non-phosphorylated AS. Biophysical measurements show that the active state is a stable dimer whilst the inactive kinase is in a monomer-dimer equilibrium, consistent with the observed structural differences at the dimer interface. We conclude that RIP2 kinase auto-phosphorylation is intimately coupled to dimerization, similar to the case of BRAF. Our results will help drug design efforts targeting RIP2 as a potential treatment for NOD2-RIP2 related inflammatory diseases.
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Affiliation(s)
| | - Luca Signor
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Saurabh Singh
- European Molecular Biology Laboratory, Grenoble, France
| | - Elisabetta Boeri Erba
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France
- * E-mail:
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2
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Tong J, Cao B, Martyn GD, Krieger JR, Taylor P, Yates B, Sidhu SS, Li SSC, Mao X, Moran MF. Protein-phosphotyrosine proteome profiling by superbinder-SH2 domain affinity purification mass spectrometry, sSH2-AP-MS. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600360] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/28/2016] [Accepted: 11/21/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Jiefei Tong
- Program in Cell Biology; Hospital for Sick Children; Toronto Canada
| | - Biyin Cao
- Department of Pharmacology; College of Pharmaceutical Sciences; Soochow University; Suzhou P. R. China
| | - Gregory D. Martyn
- Department of Molecular Genetics; University of Toronto; Toronto Canada
| | | | - Paul Taylor
- Program in Cell Biology; Hospital for Sick Children; Toronto Canada
- SPARC BioCentre; Hospital for Sick Children; Toronto Canada
| | - Bradley Yates
- Department of Molecular Genetics; University of Toronto; Toronto Canada
- Banting and Best Department of Medical Research; Donnelly Centre; University of Toronto; Toronto Canada
| | - Sachdev S. Sidhu
- Department of Molecular Genetics; University of Toronto; Toronto Canada
- Banting and Best Department of Medical Research; Donnelly Centre; University of Toronto; Toronto Canada
| | - Shawn S. C. Li
- Department of Biochemistry and Siebens-Drake Medical Research Institute; Schulich School of Medicine and Dentistry; University of Western Ontario; London Canada
| | - Xinliang Mao
- Department of Pharmacology; College of Pharmaceutical Sciences; Soochow University; Suzhou P. R. China
| | - Michael F. Moran
- Program in Cell Biology; Hospital for Sick Children; Toronto Canada
- Department of Molecular Genetics; University of Toronto; Toronto Canada
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3
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Ke Y, Garg B, Ling YC. A novel graphene-based label-free fluorescence 'turn-on' nanosensor for selective and sensitive detection of phosphorylated species in biological samples and living cells. NANOSCALE 2016; 8:4547-4556. [PMID: 26758942 DOI: 10.1039/c5nr07261a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A novel label-free fluorescence 'turn-on' nanosensor has been developed for highly selective and sensitive detection of phosphorylated species (Ps) in biological samples and living cells. The design strategy relies on the use of Ti(4+)-immobilized polydopamine (PDA) coated reduced graphene oxide (rGO@PDA-Ti(4+)) that serves as an attractive platform to bind riboflavin 5'-monophosphate molecules (FMNs) through ion-pair interactions between phosphate groups and Ti(4+). The as-prepared rGO@PDA-Ti(4+)-FMNs (nanosensor), fluoresce only weakly due to the ineffective Förster resonance energy transfer between the FMNs and rGO@PDA-Ti(4+). The experimental findings revealed that the microwave-assisted interaction of the nanosensor with α-, β-casein, ovalbumin, human serum, non-fat milk, egg white, and living cells (all containing Ps) releases FMNs (due to the high formation constant between phosphate groups and Ti(4+)), leading to an excellent fluorescence 'turn-on' response. The fluorescence spectroscopy, confocal microscopy, and MALDI-TOF MS spectrometry were used to detect Ps both qualitatively and quantitatively. Under the optimized conditions, the nanosensor showed a detection limit of ca. 118.5, 28.9, and 54.8 nM for the tryptic digests of α-, β-casein and ovalbumin, respectively. Furthermore, the standard addition method was used as a bench-mark proof for phosphopeptide quantification in egg white samples. We postulate that the present quantitative assay for Ps holds tremendous potential and may pave the way to disease diagnostics in the near future.
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Affiliation(s)
- Yaotang Ke
- Department of Chemistry, National Tsing Hua University, Kuang-Fu Road, Hsinchu, 30013, Taiwan.
| | - Bhaskar Garg
- Department of Chemistry, National Tsing Hua University, Kuang-Fu Road, Hsinchu, 30013, Taiwan.
| | - Yong-Chien Ling
- Department of Chemistry, National Tsing Hua University, Kuang-Fu Road, Hsinchu, 30013, Taiwan. and Institute of Nano Engineering and Microsystem, National Tsing Hua University, Kuang-Fu Road, Hsinchu, 30013, Taiwan
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4
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St-Germain JR, Taylor P, Zhang W, Li Z, Ketela T, Moffat J, Neel BG, Trudel S, Moran MF. Differential regulation of FGFR3 by PTPN1 and PTPN2. Proteomics 2014; 15:419-33. [PMID: 25311528 DOI: 10.1002/pmic.201400259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/04/2014] [Accepted: 10/08/2014] [Indexed: 11/06/2022]
Abstract
Aberrant expression and activation of FGFR3 is associated with disease states including bone dysplasia and malignancies of bladder, cervix, and bone marrow. MS analysis of protein-phosphotyrosine in multiple myeloma cells revealed a prevalent phosphorylated motif, D/EYYR/K, derived from the kinase domain activation loops of tyrosine kinases including FGFR3 corresponding to a recognition sequence of protein-tyrosine phosphatase PTPN1. Knockdown of PTPN1 or the related enzyme PTPN2 by RNAi resulted in ligand-independent activation of FGFR3. Modulation of FGFR3 activation loop phosphorylation by both PTPN1 and PTPN2 was a function of receptor trafficking and phosphotyrosine phosphatase (PTP) compartmentalization. The FGFR3 activation loop motif DYYKK(650) is altered to DYYKE(650) in the oncogenic variant FGFR3(K650E) , and consequently it is constitutively fully activated and unaffected by activation loop phosphorylation. FGFR3(K650E) was nevertheless remarkably sensitive to negative regulation by PTPN1 and PTPN2. This suggests that in addition to modulating FGFR3 phosphorylation, PTPN1 and PTPN2 constrain the kinase domain by fostering an inactive-state. Loss of this constraint in response to ligand or impaired PTPN1/N2 may initiate FGFR3 activation. These results suggest a model wherein PTP expression levels may define conditions that select for ectopic FGFR3 expression and activation during tumorigenesis.
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Affiliation(s)
- Jonathan R St-Germain
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Canada
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5
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Ceresa BP, Peterson JL. Cell and molecular biology of epidermal growth factor receptor. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 313:145-78. [PMID: 25376492 DOI: 10.1016/b978-0-12-800177-6.00005-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The epidermal growth factor receptor (EGFR) has been one of the most intensely studied cell surface receptors due to its well-established roles in developmental biology, tissue homeostasis, and cancer biology. The EGFR has been critical for creating paradigms for numerous aspects of cell biology, such as ligand binding, signal transduction, and membrane trafficking. Despite this history of discovery, there is a continual stream of evidence that only the surface has been scratched. New ways of receptor regulation continue to be identified, each of which is a potential molecular target for manipulating EGFR signaling and the resultant changes in cell and tissue biology. This chapter is an update on EGFR-mediated signaling, and describes some recent developments in the regulation of receptor biology.
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Affiliation(s)
- Brian P Ceresa
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Joanne L Peterson
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
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6
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Chen TC, Liu YW, Huang YH, Yeh YC, Chou TY, Wu YC, Wu CC, Chen YR, Cheng HC, Lu PJ, Lai JM, Huang CYF. Protein phosphorylation profiling using an in situ proximity ligation assay: phosphorylation of AURKA-elicited EGFR-Thr654 and EGFR-Ser1046 in lung cancer cells. PLoS One 2013; 8:e55657. [PMID: 23520446 PMCID: PMC3592865 DOI: 10.1371/journal.pone.0055657] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 01/03/2013] [Indexed: 01/01/2023] Open
Abstract
The epidermal growth factor receptor (EGFR), which is up-regulated in lung cancer, involves the activation of mitogenic signals and triggers multiple signaling cascades. To dissect these EGFR cascades, we used 14 different phospho-EGFR antibodies to quantify protein phosphorylation using an in situ proximity ligation assay (in situ PLA). Phosphorylation at EGFR-Thr654 and -Ser1046 was EGF-dependent in the wild-type (WT) receptor but EGF-independent in a cell line carrying the EGFR-L858R mutation. Using a ProtoAarray™ containing ∼5000 recombinant proteins on the protein chip, we found that AURKA interacted with the EGFR-L861Q mutant. Moreover, overexpression of EGFR could form a complex with AURKA, and the inhibitors of AURKA and EGFR decreased EGFR-Thr654 and -Ser1046 phosphorylation. Immunohistochemical staining of stage I lung adenocarcinoma tissues demonstrated a positive correlation between AURKA expression and phosphorylation of EGFR at Thr654 and Ser1046 in EGFR-mutant specimens, but not in EGFR-WT specimens. The interplay between EGFR and AURKA provides an explanation for the difference in EGF dependency between EGFR-WT and EGFR-mutant cells and may provide a new therapeutic strategy for lung cancer patients carrying EGFR mutations.
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Affiliation(s)
- Tzu-Chi Chen
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yu-Wen Liu
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Yei-Hsuan Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chen Yeh
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Teh-Ying Chou
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Chung Wu
- Division of Thoracic Surgery, Department of Surgery, Veterans General Hospital, Taipei, Taiwan
| | - Chun-Chi Wu
- Institute of Medicine, Chung-Shan Medical University, Taichung, Taiwan
| | - Yi-Rong Chen
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Hui-Chuan Cheng
- Institute of Clinical Medicine, Medical College, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Jung Lu
- Institute of Clinical Medicine, Medical College, National Cheng Kung University, Tainan, Taiwan
| | - Jin-Mei Lai
- Department of Life Science, Fu-Jen Catholic University, Taipei, Taiwan
| | - Chi-Ying F. Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan
- * E-mail:
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7
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Senevirathne C, Pflum MKH. Biotinylated phosphoproteins from kinase-catalyzed biotinylation are stable to phosphatases: implications for phosphoproteomics. Chembiochem 2013; 14:381-7. [PMID: 23335220 PMCID: PMC4524292 DOI: 10.1002/cbic.201200626] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Indexed: 11/11/2022]
Abstract
Kinase-catalyzed protein phosphorylation is involved in a wide variety of cellular events. Development of methods to monitor phosphorylation is critical to understand cell biology. Our lab recently discovered kinase-catalyzed biotinylation, where ATP-biotin is utilized by kinases to label phosphopeptides or phosphoproteins with a biotin tag. To exploit kinase-catalyzed biotinylation for phosphoprotein purification and identification in a cellular context, the susceptibility of the biotin tag to phosphatases was characterized. We found that the phosphorylbiotin group on peptide and protein substrates was relatively insensitive to protein phosphatases. To understand how phosphatase stability would impact phosphoproteomics research applications, kinase-catalyzed biotinylation of cell lysates was performed in the presence of kinase or phosphatase inhibitors. We found that biotinylation with ATP-biotin was sensitive to inhibitors, although with variable effects compared to ATP phosphorylation. The results suggest that kinase-catalyzed biotinylation is well suited for phosphoproteomics studies, with particular utility towards monitoring low-abundance phosphoproteins or characterizing the influence of inhibitor drugs on protein phosphorylation.
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Affiliation(s)
| | - Mary Kay H. Pflum
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, Fax: (+)
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8
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Courcelles M, Bridon G, Lemieux S, Thibault P. Occurrence and Detection of Phosphopeptide Isomers in Large-Scale Phosphoproteomics Experiments. J Proteome Res 2012; 11:3753-65. [DOI: 10.1021/pr300229m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mathieu Courcelles
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Gaëlle Bridon
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Sébastien Lemieux
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Pierre Thibault
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
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9
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Rucevic M, Hixson D, Josic D. Mammalian plasma membrane proteins as potential biomarkers and drug targets. Electrophoresis 2011; 32:1549-64. [PMID: 21706493 DOI: 10.1002/elps.201100212] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Defining the plasma membrane proteome is crucial to understand the role of plasma membrane in fundamental biological processes. Change in membrane proteins is one of the first events that take place under pathological conditions, making plasma membrane proteins a likely source of potential disease biomarkers with prognostic or diagnostic potential. Membrane proteins are also potential targets for monoclonal antibodies and other drugs that block receptors or inhibit enzymes essential to the disease progress. Despite several advanced methods recently developed for the analysis of hydrophobic proteins and proteins with posttranslational modifications, integral membrane proteins are still under-represented in plasma membrane proteome. Recent advances in proteomic investigation of plasma membrane proteins, defining their roles as diagnostic and prognostic disease biomarkers and as target molecules in disease treatment, are presented.
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Affiliation(s)
- Marijana Rucevic
- COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI, USA
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10
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Tran BQ, Hernandez C, Waridel P, Potts A, Barblan J, Lisacek F, Quadroni M. Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides. J Proteome Res 2010; 10:800-11. [DOI: 10.1021/pr100951t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bao Quoc Tran
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Celine Hernandez
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Patrice Waridel
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Alexandra Potts
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Jachen Barblan
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Frederique Lisacek
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
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11
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Zimman A, Chen SS, Komisopoulou E, Titz B, Martínez-Pinna R, Kafi A, Berliner JA, Graeber TG. Activation of aortic endothelial cells by oxidized phospholipids: a phosphoproteomic analysis. J Proteome Res 2010; 9:2812-24. [PMID: 20307106 DOI: 10.1021/pr901194x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Previous studies have shown that oxidized products of the phospholipid PAPC (Ox-PAPC) are strong activators of aortic endothelial cells and play an important role in atherosclerosis and other inflammatory diseases. We and others have demonstrated that Ox-PAPC activates specific signaling pathways and regulates a large number of genes. Using a phosphoproteomic approach based on phosphopeptide enrichment and mass spectrometry analysis, we identified candidate changes in Ox-PAPC-induced protein phosphorylation of 228 proteins. Functional annotation of these proteins showed an enrichment of the regulation of cytoskeleton, junctional components, and tyrosine kinases, all of which may contribute to the phenotypic and molecular changes observed in endothelial cells treated with Ox-PAPC. Many changes in protein phosphorylation induced by Ox-PAPC are reported here for the first time and provide new insights into the mechanism of activation by oxidized lipids, including phosphorylation-based signal transduction.
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Affiliation(s)
- Alejandro Zimman
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095-1770, USA
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12
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Cabodi S, Di Stefano P, Leal MDPC, Tinnirello A, Bisaro B, Morello V, Damiano L, Aramu S, Repetto D, Tornillo G, Defilippi P. Integrins and signal transduction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 674:43-54. [PMID: 20549939 DOI: 10.1007/978-1-4419-6066-5_5] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Integrin signaling has a critical function in organizing cells in tissues during both embryonic development and tissue repair. Following their binding to the extracellular ligands, the intracellular signaling pathways triggered by integrins are directed to two major functions: organization of the actin cytoskeleton and regulation of cell behaviour including survival, differentiation and growth. Basic research conducted in the past twelve years has lead to remarkable breakthroughs in this field. Integrins are catalytically inactive and translate positional cues into biochemical signals by direct and/or functional association with intracellular adaptors, cytosolic tyrosine kinases or growth factor and cytokine receptors. The purpose of this chapter is to highlight recent experimental and conceptual advances in integrin signaling with particular emphasis on the ability of integrins to regulate Fak/Src family kinases (SFKs) activation and the cross-talk with soluble growth factors receptors and cytokines.
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Affiliation(s)
- Sara Cabodi
- Molecular and Biotechnology Center and Department of Genetics, Biology and Biochemistry, University of Torino, Via Nizza 52, 10126 Torino, Italy
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13
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Cunningham DL, Sweet SMM, Cooper HJ, Heath JK. Differential phosphoproteomics of fibroblast growth factor signaling: identification of Src family kinase-mediated phosphorylation events. J Proteome Res 2010; 9:2317-28. [PMID: 20225815 PMCID: PMC2950672 DOI: 10.1021/pr9010475] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Indexed: 01/12/2023]
Abstract
Activation of signal transduction by the receptor tyrosine kinase, fibroblast growth factor receptor (FGFR), results in a cascade of protein-protein interactions that rely on the occurrence of specific tyrosine phosphorylation events. One such protein recruited to the activated receptor complex is the nonreceptor tyrosine kinase, Src, which is involved in both initiation and termination of further signaling events. To gain a further understanding of the tyrosine phosphorylation events that occur during FGF signaling, with a specific focus on those that are dependent on Src family kinase (SFK) activity, we have applied SILAC combined with chemical inhibition of SFK activity to search for phosphorylation events that are dependent on SFK activity in FGF stimulated cells. In addition, we used a more targeted approach to carry out high coverage phosphopeptide mapping of one Src substrate protein, the multifunctional adaptor Dok1, and to identify SFK-dependent Dok1 binding partners. From these analyses we identify 80 SFK-dependent phosphorylation events on 40 proteins. We further identify 18 SFK-dependent Dok1 interactions and 9 SFK-dependent Dok1 phosphorylation sites, 6 of which had not previously been known to be SFK-dependent.
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Affiliation(s)
| | | | - Helen J. Cooper
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - John K. Heath
- To whom correspondence should be addressed. Prof. John K. Heath, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K. Telephone: +44 (0)121 414 7533. Fax: +44 (0)121 414 5925.
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14
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Chen CT, Chen YC. Functional magnetic nanoparticle-based label free fluorescence detection of phosphorylated species. Chem Commun (Camb) 2010; 46:5674-6. [DOI: 10.1039/c0cc00637h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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15
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Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition. Proc Natl Acad Sci U S A 2009; 106:20127-32. [PMID: 19901323 DOI: 10.1073/pnas.0910957106] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Signaling by growth factor receptor tyrosine kinases is manifest through networks of proteins that are substrates and/or bind to the activated receptors. FGF receptor-3 (FGFR3) is a drug target in a subset of human multiple myelomas (MM) and is mutationally activated in some cervical and colon and many bladder cancers and in certain skeletal dysplasias. To define the FGFR3 network in multiple myeloma, mass spectrometry was used to identify and quantify phosphotyrosine (pY) sites modulated by FGFR3 activation and inhibition in myeloma-derived KMS11 cells. Label-free quantification of peptide ion currents indicated the activation of FGFR3 by phosphorylation of tandem tyrosines in the kinase domain activation loop when cellular pY phosphatases were inhibited by pervanadate. Among the 175 proteins that accumulated pY in response to pervanadate was a subset of 52 including FGFR3 that contained a total of 61 pY sites that were sensitive to inhibition by the FGFR3 inhibitor PD173074. The FGFR3 isoform containing the tandem pY motif in its activation loop was targeted by PD173074. Forty of the drug-sensitive pY sites, including two located within the 35-residue cytoplasmic domain of the transmembrane growth factor binding proteoglycan (and multiple myeloma biomarker) Syndecan-1/CD138, were also stimulated in cells treated with the ligand FGF1, providing additional validation of their link to FGFR3. The identification of these overlapping sets of co-modulated tyrosine phosphorylations presents an outline of an FGFR3 network in the MM model and demonstrates the potential for pharmacodynamic monitoring by label-free quantitative phospho-proteomics.
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16
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Tong J, Taylor P, Peterman SM, Prakash A, Moran MF. Epidermal growth factor receptor phosphorylation sites Ser991 and Tyr998 are implicated in the regulation of receptor endocytosis and phosphorylations at Ser1039 and Thr1041. Mol Cell Proteomics 2009; 8:2131-44. [PMID: 19531499 PMCID: PMC2742444 DOI: 10.1074/mcp.m900148-mcp200] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aberrant expression, activation, and down-regulation of the epidermal growth factor receptor (EGFR) have causal roles in many human cancers, and post-translational modifications including phosphorylation and ubiquitination and protein-protein interactions directly modulate EGFR function. Quantitative mass spectrometric analyses including selected reaction monitoring (also known as multiple reaction monitoring) were applied to the EGFR and associated proteins. In response to epidermal growth factor (EGF) stimulation of cells, phosphorylations at EGFR Ser991 and Tyr998 accumulated more slowly than at receptor sites involved in RAS-ERK signaling. Phosphorylation-deficient mutant receptors S991A and Y998F activated ERK in response to EGF but were impaired for receptor endocytosis. Consistent with these results, the mutant receptors retained a network of interactions with known signaling proteins including EGF-stimulated binding to the adaptor GRB2. Compared with wild type EGFR the Y998F variant had diminished EGF-stimulated interaction with the ubiquitin E3 ligase CBL, and the S991A variant had decreased associated ubiquitin. The endocytosis-defective mutant receptors were found to have elevated phosphorylation at positions Ser1039 and Thr1041. These residues reside in a serine/threonine-rich region of the receptor previously implicated in p38 mitogen-activated protein kinase-dependent stress/cytokine-induced EGFR internalization and recycling (Zwang, Y., and Yarden, Y. (2006) p38 MAP kinase mediates stress-induced internalization of EGFR: implications for cancer chemotherapy. EMBO J. 25, 4195–4206). EGF-induced phosphorylations at Ser1039 and Thr1041 were blocked by treatment of cells with SB-202190, a selective inhibitor of p38. These results suggest that coordinated phosphorylation of EGFR involving sites Tyr998, Ser991, Ser1039, and Thr1041 governs the trafficking of EGF receptors. This reinforces the notion that EGFR function is manifest through spatially and temporally controlled protein-protein interactions and phosphorylations.
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Affiliation(s)
- Jiefei Tong
- Program in Molecular Structure and Function, The Hospital For Sick Children, and The McLaughlin Centre For Molecular Medicine, Toronto, Ontario M5G 1L7, Canada
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Oellerich T, Grønborg M, Neumann K, Hsiao HH, Urlaub H, Wienands J. SLP-65 phosphorylation dynamics reveals a functional basis for signal integration by receptor-proximal adaptor proteins. Mol Cell Proteomics 2009; 8:1738-50. [PMID: 19372136 DOI: 10.1074/mcp.m800567-mcp200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding intracellular signal transduction by cell surface receptors requires information about the precise order of relevant modifications on the early transducer elements. Here we introduce the B cell line DT40 and its genetically engineered variants as a model system to determine and functionally characterize post-translational protein modifications in general. This is accomplished by a customized strategy that combines mass spectrometric analyses of protein modifications with subsequent mutational studies. When applied to the B cell receptor (BCR)-proximal effector SLP-65, this approach uncovered a differential and highly dynamic engagement of numerous newly identified phospho-acceptor sites. Some of them serve as kinase substrates in resting cells and undergo rapid dephosphorylation upon BCR ligation. Stimulation-induced phosphorylation of SLP-65 can be early and transient, or early and sustained, or late. Functional elucidation of conspicuous phosphorylation at serine 170 in SLP-65 revealed a BCR-distal checkpoint for some but not all possible B cell responses. Our data show that SLP-65 phosphorylation acts upstream for signal initiation and also downstream during selective processing of the BCR signal. Such a phenomenon defines a receptor-specific signal integrator.
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Affiliation(s)
- Thomas Oellerich
- Institute of Cellular and Molecular Immunology, Georg August University of Göttingen, Göttingen, Germany
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Cabodi S, Morello V, Masi A, Cicchi R, Broggio C, Distefano P, Brunelli E, Silengo L, Pavone F, Arcangeli A, Turco E, Tarone G, Moro L, Defilippi P. Convergence of integrins and EGF receptor signaling via PI3K/Akt/FoxO pathway in early gene Egr-1 expression. J Cell Physiol 2008; 218:294-303. [PMID: 18844239 DOI: 10.1002/jcp.21603] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The early gene early growth response (Egr-1), a broadly expressed member of the zing-finger family of transcription factors, is induced in many cell types by a variety of growth and differentiation stimuli, including epidermal growth factor (EGF). Here we demonstrate that Egr-1 expression is mainly regulated by integrin-mediated adhesion. Integrin-dependent adhesion plays a dual role in Egr-1 regulation, either being sufficient "per se" to induce Egr-1, or required for EGF-dependent expression of Egr-1, which occurs only in adherent cells and not in cells in suspension. To dissect the molecular basis of integrin-dependent Egr-1 regulation, we show by FLIM-based FRET that in living cells beta1-integrin associates with the EGF receptor (EGFR) and that EGF further increases the extent complex formation. Interestingly, Egr-1 induction depends on integrin-dependent PI3K/Akt activation, as indicated by the decrease in Egr-1 levels in presence of the pharmacological inhibitor LY294002, the kinase-defective Akt mutant and Akt1/2 shRNAs. Indeed, upon adhesion activated Akt translocates into the nucleus and phosphorylates FoxO1, a Forkhead transcription factors. Consistently, FoxO1silencing results in Egr-1-increased levels, indicating that FoxO1 behaves as a negative regulator of Egr-1 expression. These data demonstrate that integrin/EGFR cross-talk is required for expression of Egr-1 through a novel regulatory cascade involving the activation of the PI3K/Akt/Forkhead pathway.
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Affiliation(s)
- Sara Cabodi
- Centro di Biotecnologie Molecolari and Dipartimento di Genetica, Biologia e Biochimica, Università di Torino, Torino, Italy
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Pan C, Gnad F, Olsen JV, Mann M. Quantitative phosphoproteome analysis of a mouse liver cell line reveals specificity of phosphatase inhibitors. Proteomics 2008; 8:4534-46. [PMID: 18846507 DOI: 10.1002/pmic.200800105] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The liver is a central organ involved in many aspects of physiology and disease. Signaling properties of hepatocytes, the main liver cell type, are of special interest in metabolic diseases and in regeneration. For this reason we investigated the phosphoproteome of the mouse liver cell line Hepa1-6 by stable isotope labeling by amino acids in cell culture (SILAC) and high resolution MS. Using stringent statistical evaluation criteria, we obtained 5433 phosphorylation sites on 1808 proteins. The phosphoproteome encompasses all major protein classes, including a large number of transcription factors. We compared control and phosphatase inhibitor treated cells by SILAC. This enabled ready identification of in vivo phosphorylation sites by sequencing the more abundant, inhibitor induced version of the peptide while still observing the endogenous version. We employed a mixture of pervanadate for blocking protein tyrosine phosphatases (PTPs) and calyculin A and deltamethrin for blocking the activities of serine/threonine phosphatases. Interestingly, these commonly used inhibitors in standard concentrations affected only 28% of the phosphopeptides by at least two-fold. The unaffected sites may be substrates of phosphatases that are not efficiently inhibited, have slow kinetic or sites that are almost stoichiometric in normally growing cells. Finally, we devised a triple labeling strategy comprising control cells, stimulated cells, and phosphatase treated cells to derive an upper bound on phosphorylation occupancy.
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Affiliation(s)
- Cuiping Pan
- Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Martinsried, Germany
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20
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Atsriku C, Britton DJ, Held JM, Schilling B, Scott GK, Gibson BW, Benz CC, Baldwin MA. Systematic mapping of posttranslational modifications in human estrogen receptor-alpha with emphasis on novel phosphorylation sites. Mol Cell Proteomics 2008; 8:467-80. [PMID: 18984578 DOI: 10.1074/mcp.m800282-mcp200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A systematic study of posttranslational modifications of the estrogen receptor isolated from the MCF-7 human breast cancer cell line is reported. Proteolysis with multiple enzymes, mass spectrometry, and tandem mass spectrometry achieved very high sequence coverage for the full-length 66-kDa endogenous protein from estradiol-treated cell cultures. Nine phosphorylated serine residues were identified, three of which were previously unreported and none of which were previously observed by mass spectrometry by any other laboratory. Two additional modified serine residues were identified in recombinant protein, one previously reported but not observed here in endogenous protein and the other previously unknown. Although major emphasis was placed on identifying new phosphorylation sites, N-terminal loss of methionine accompanied by amino acetylation and a lysine side chain acetylation (or possibly trimethylation) were also detected. The use of both HPLC-ESI and MALDI interfaced to different mass analyzers gave higher sequence coverage and identified more sites than could be achieved by either method alone. The estrogen receptor is critical in the development and progression of breast cancer. One previously unreported phosphorylation site identified here was shown to be strongly dependent on estradiol, confirming its potential significance to breast cancer. Greater knowledge of this array of posttranslational modifications of estrogen receptor, particularly phosphorylation, will increase our understanding of the processes that lead to estradiol-induced activation of this protein and may aid the development of therapeutic strategies for management of hormone-dependent breast cancer.
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Morandell S, Stasyk T, Skvortsov S, Ascher S, Huber LA. Quantitative proteomics and phosphoproteomics reveal novel insights into complexity and dynamics of the EGFR signaling network. Proteomics 2008; 8:4383-401. [DOI: 10.1002/pmic.200800204] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Phosphorylation is one of the most relevant and ubiquitous post-translational modifications. Despite its relevance, the analysis of protein phosphorylation has been revealed as one of the most challenging tasks due to its highly dynamic nature and low stoichiometry. However, the development and introduction of new analytical methods are modifying rapidly and substantially this field. Especially important has been the introduction of more sensitive and specific methods for phosphoprotein and phosphopeptide purification as well as the use of more sensitive and accurate MS-based analytical methods. The integration of both approaches has enabled large-scale phosphoproteome studies to be performed, an unimaginable task few years ago. Additionally, methods originally developed for differential proteomics have been adapted making the study of the highly dynamic nature of protein phosphorylation feasible. This review aims at offering an overview on the most frequently used methods in phosphoprotein and phosphopeptide enrichment as well as on the most recent MS-based analysis strategies. Current strategies for quantitative phosphoproteomics and the study of the dynamics of protein phosphorylation are highlighted.
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Affiliation(s)
- Alberto Paradela
- Departamento de Proteómica, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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Palumbo AM, Tepe JJ, Reid GE. Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides. J Proteome Res 2008; 7:771-9. [DOI: 10.1021/pr0705136] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Amanda M. Palumbo
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Jetze J. Tepe
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gavin E. Reid
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Schuchardt S, Borlak J. Quantitative mass spectrometry to investigate epidermal growth factor receptor phosphorylation dynamics. MASS SPECTROMETRY REVIEWS 2008; 27:51-65. [PMID: 18023079 DOI: 10.1002/mas.20155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Identifying proteins of signaling networks has received much attention, because an array of biological processes are entirely dependent on protein cross-talk and protein-protein interactions. Protein posttranslational modifications (PTM) add an additional layer of complexity, resulting in complex signaling networks. Of particular interest to our working group are the signaling networks of epidermal growth factor (EGF) receptor, a transmembrane receptor tyrosine kinase involved in various cellular processes, including cell proliferation, differentiation, and survival. Ligand binding to the N-terminal residue of the extracellular domain of EGF receptor induces conformational changes, dimerization, and (auto)-phosphorylation of intracellular tyrosine residues. In addition, activated EGF receptor may positively affect survival pathways, and thus determines the pathways for tumor growth and progression. Notably, in many human malignancies exaggerated EGF receptor activities are commonly observed. An understanding of the mechanism that results in aberrant phosphorylation of EGF receptor tyrosine residues and derived signaling cascades is crucial for an understanding of molecular mechanisms in cancer development. Here, we summarize recent labeling methods and discuss the difficulties in quantitative MS-based phosphorylation assays to probe for receptor tyrosine kinase (RTK) activity. We also review recent advances in sample preparation to investigate membrane-bound RTKs, MS-based detection of phosphopeptides, and the diligent use of different quantitative methods for protein labeling.
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Affiliation(s)
- Sven Schuchardt
- Department of Drug Research and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Strasse 1, Hannover, Germany
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de Laurentiis A, Donovan L, Arcaro A. Lipid rafts and caveolae in signaling by growth factor receptors. Open Biochem J 2007; 1:12-32. [PMID: 18949068 PMCID: PMC2570545 DOI: 10.2174/1874091x00701010012] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 08/15/2007] [Accepted: 08/16/2007] [Indexed: 12/29/2022] Open
Abstract
Lipid rafts and caveolae are microdomains of the plasma membrane enriched in sphingolipids and cholesterol, and hence are less fluid than the remainder of the membrane. Caveolae have an invaginated structure, while lipid rafts are flat regions of the membrane. The two types of microdomains have different protein compositions (growth factor receptors and their downstream molecules) suggesting that lipid rafts and caveolae have a role in the regulation of signaling by these receptors. The purpose of this review is to discuss this model, and the implications that it might have regarding a potential role for lipid rafts and caveolae in human cancer. Particular attention will be paid to the epidermal growth factor receptor, for which the largest amount of information is available. It has been proposed that caveolins act as tumor suppressors. The role of lipid rafts is less clear, but they seem to be capable of acting as 'signaling platforms', in which signal initiation and propagation can occur efficiently.
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Affiliation(s)
- Angela de Laurentiis
- Division of Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Lorna Donovan
- Division of Medicine, Imperial College Faculty of Medicine, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
| | - Alexandre Arcaro
- Division of Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
- Division of Medicine, Imperial College Faculty of Medicine, Hammersmith Hospital, Du Cane Road, London W12 ONN, UK
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