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Watson GM, Lucas WAH, Gunzburg MJ, Wilce JA. Insight into the Selectivity of the G7-18NATE Inhibitor Peptide for the Grb7-SH2 Domain Target. Front Mol Biosci 2017; 4:64. [PMID: 29018805 PMCID: PMC5623053 DOI: 10.3389/fmolb.2017.00064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022] Open
Abstract
Growth factor receptor bound protein 7 (Grb7) is an adaptor protein with established roles in the progression of both breast and pancreatic cancers. Through its C-terminal SH2 domain, Grb7 binds to phosphorylated tyrosine kinases to promote proliferative and migratory signaling. Here, we investigated the molecular basis for the specificity of a Grb7 SH2-domain targeted peptide inhibitor. We identified that arginine 462 in the BC loop is unique to Grb7 compared to Grb2, another SH2 domain bearing protein that shares the same consensus binding motif as Grb7. Using surface plasmon resonance we demonstrated that Grb7-SH2 binding to G7-18NATE is reduced 3.3-fold when the arginine is mutated to the corresponding Grb2 amino acid. The reverse mutation in Grb2-SH2 (serine to arginine), however, was insufficient to restore binding of G7-18NATE to Grb2-SH2. Further, using a microarray, we confirmed that G7-18NATE is specific for Grb7 over a panel of 79 SH2 domains, and identified that leucine at the βD6 position may also be a requirement for Grb7-SH2 binding. This study provides insight into the specificity defining features of Grb7 for the inhibitor molecule G7-18NATE, that will assist in the development of improved Grb7 targeted inhibitors.
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Affiliation(s)
| | | | | | - Jacqueline A. Wilce
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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52
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Huang Z, Tan Y, Gu J, Liu Y, Song L, Niu J, Zhao L, Srinivasan L, Lin Q, Deng J, Li Y, Conklin DJ, Neubert TA, Cai L, Li X, Mohammadi M. Uncoupling the Mitogenic and Metabolic Functions of FGF1 by Tuning FGF1-FGF Receptor Dimer Stability. Cell Rep 2017; 20:1717-1728. [PMID: 28813681 PMCID: PMC5821125 DOI: 10.1016/j.celrep.2017.06.063] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/11/2017] [Accepted: 06/20/2017] [Indexed: 12/21/2022] Open
Abstract
The recent discovery of metabolic roles for fibroblast growth factor 1 (FGF1) in glucose homeostasis has expanded the functions of this classically known mitogen. To dissect the molecular basis for this functional pleiotropy, we engineered an FGF1 partial agonist carrying triple mutations (FGF1ΔHBS) that diminished its ability to induce heparan sulfate (HS)-assisted FGF receptor (FGFR) dimerization and activation. FGF1ΔHBS exhibited a severely reduced proliferative potential, while preserving the full metabolic activity of wild-type FGF1 in vitro and in vivo. Hence, suboptimal FGFR activation by a weak FGF1-FGFR dimer is sufficient to evoke a metabolic response, whereas full FGFR activation by stable and sustained dimerization is required to elicit a mitogenic response. In addition to providing a physical basis for the diverse activities of FGF1, our findings will impact ongoing drug discoveries targeting FGF1 and related FGFs for the treatment of a variety of human diseases.
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Affiliation(s)
- Zhifeng Huang
- School of Pharmacy & Center for Structural Biology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yi Tan
- School of Pharmacy & Center for Structural Biology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Pediatric Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Junlian Gu
- Pediatric Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA; Diabetes and Obesity Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Yang Liu
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Lintao Song
- School of Pharmacy & Center for Structural Biology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jianlou Niu
- School of Pharmacy & Center for Structural Biology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Longwei Zhao
- School of Pharmacy & Center for Structural Biology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Lakshmi Srinivasan
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Qian Lin
- School of Pharmacy & Center for Structural Biology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Pediatric Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Jingjing Deng
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Yang Li
- Amgen, Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA
| | - Daniel J Conklin
- Diabetes and Obesity Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Thomas A Neubert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Lu Cai
- Pediatric Research Institute, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Xiaokun Li
- School of Pharmacy & Center for Structural Biology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Moosa Mohammadi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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53
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APPL1 is a multifunctional endosomal signaling adaptor protein. Biochem Soc Trans 2017; 45:771-779. [PMID: 28620038 DOI: 10.1042/bst20160191] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/17/2017] [Accepted: 03/22/2017] [Indexed: 11/17/2022]
Abstract
Endosomal adaptor proteins are important regulators of signaling pathways underlying many biological processes. These adaptors can integrate signals from multiple pathways via localization to specific endosomal compartments, as well as through multiple protein-protein interactions. One such adaptor protein that has been implicated in regulating signaling pathways is the adaptor protein containing a pleckstrin homology (PH) domain, phosphotyrosine-binding (PTB) domain, and leucine zipper motif 1 (APPL1). APPL1 localizes to a subset of Rab5-positive endosomes through its Bin-Amphiphysin-Rvs and PH domains, and it coordinates signaling pathways through its interaction with many signaling receptors and proteins through its PTB domain. This review discusses our current understanding of the role of APPL1 in signaling and trafficking, as well as highlights recent work into the function of APPL1 in cell migration and adhesion.
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Del Piccolo N, Hristova K. Quantifying the Interaction between EGFR Dimers and Grb2 in Live Cells. Biophys J 2017; 113:1353-1364. [PMID: 28734476 DOI: 10.1016/j.bpj.2017.06.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/19/2017] [Accepted: 06/12/2017] [Indexed: 12/21/2022] Open
Abstract
Adaptor proteins are a class of cytoplasmic proteins that bind to phosphorylated residues in receptor tyrosine kinases and trigger signaling cascades that control critically important cellular processes, such as cell survival, growth, differentiation, and motility. Here, we seek to characterize the interaction between epidermal growth factor receptor (EGFR) and the cytoplasmic adaptor protein growth factor receptor-bound protein 2 (Grb2) in a cellular context. To do so, we explore the utility of a highly biologically relevant model system, mammalian cells under reversible osmotic stress, and a recently introduced Förster resonance energy transfer microscopy method, fully quantified spectral imaging. We present a method that allows us to quantify the stoichiometry and the association constant of the EGFR-Grb2 binding interaction in the plasma membrane, in the presence and absence of activating ligand. The method that we introduce can have broad utility in membrane protein research, as it can be applied to different membrane protein-cytoplasmic protein pairs.
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Affiliation(s)
- Nuala Del Piccolo
- Department of Materials Science and Engineering and Institute for NanoBio Technology, Johns Hopkins University, Baltimore, Maryland
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBio Technology, Johns Hopkins University, Baltimore, Maryland.
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55
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van der Meulen T, Swarts S, Fischer W, van der Geer P. Identification of STS-1 as a novel ShcA-binding protein. Biochem Biophys Res Commun 2017; 490:1334-1339. [PMID: 28690151 DOI: 10.1016/j.bbrc.2017.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022]
Abstract
ShcA is a cytoplasmic signaling protein that supports signal transduction by receptor protein-tyrosine kinases by providing auxiliary tyrosine phosphorylation sites that engage additional signaling proteins. The principal binding partner for tyrosine phosphorylation sites on ShcA is Grb2. In the current study, we have used phosphotyrosine-containing peptides to isolate and identify STS-1 as a novel ShcA-binding protein. Our results further show that the interaction between STS-1 and ShcA is regulated in response to EGF receptor activation.
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Affiliation(s)
- Talitha van der Meulen
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA
| | - Spencer Swarts
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA
| | - Wolfgang Fischer
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Peter van der Geer
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA.
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Sanchez-Quiles V, Akimov V, Osinalde N, Francavilla C, Puglia M, Barrio-Hernandez I, Kratchmarova I, Olsen JV, Blagoev B. Cylindromatosis Tumor Suppressor Protein (CYLD) Deubiquitinase is Necessary for Proper Ubiquitination and Degradation of the Epidermal Growth Factor Receptor. Mol Cell Proteomics 2017; 16:1433-1446. [PMID: 28572092 DOI: 10.1074/mcp.m116.066423] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/08/2017] [Indexed: 11/06/2022] Open
Abstract
Cylindromatosis tumor suppressor protein (CYLD) is a deubiquitinase, best known as an essential negative regulator of the NFkB pathway. Previous studies have suggested an involvement of CYLD in epidermal growth factor (EGF)-dependent signal transduction as well, as it was found enriched within the tyrosine-phosphorylated complexes in cells stimulated with the growth factor. EGF receptor (EGFR) signaling participates in central cellular processes and its tight regulation, partly through ubiquitination cascades, is decisive for a balanced cellular homeostasis. Here, using a combination of mass spectrometry-based quantitative proteomic approaches with biochemical and immunofluorescence strategies, we demonstrate the involvement of CYLD in the regulation of the ubiquitination events triggered by EGF. Our data show that CYLD regulates the magnitude of ubiquitination of several major effectors of the EGFR pathway by assisting the recruitment of the ubiquitin ligase Cbl-b to the activated EGFR complex. Notably, CYLD facilitates the interaction of EGFR with Cbl-b through its Tyr15 phosphorylation in response to EGF, which leads to fine-tuning of the receptor's ubiquitination and subsequent degradation. This represents a previously uncharacterized strategy exerted by this deubiquitinase and tumors suppressor for the negative regulation of a tumorigenic signaling pathway.
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Affiliation(s)
- Virginia Sanchez-Quiles
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Vyacheslav Akimov
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nerea Osinalde
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Chiara Francavilla
- §Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michele Puglia
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Inigo Barrio-Hernandez
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Irina Kratchmarova
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper V Olsen
- §Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Blagoy Blagoev
- From the ‡Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark;
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Abstract
SH2 domains first shed light on the key role of modular binding domains in cell signaling. Much of what we now know about the logic and design principles underlying cell signaling mechanisms, and how such mechanisms might have evolved, can be traced back to early work on SH2 domains. Here we briefly outline several key concepts that emerged from such studies.
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Affiliation(s)
- Bruce J Mayer
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, Farmington, CT, USA.
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58
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Zhao Z, Tan SH, Machiyama H, Kawauchi K, Araki K, Hirata H, Sawada Y. Association between tensin 1 and p130Cas at focal adhesions links actin inward flux to cell migration. Biol Open 2016; 5:499-506. [PMID: 27029899 PMCID: PMC4890666 DOI: 10.1242/bio.016428] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cell migration is a highly dynamic process that plays pivotal roles in both physiological and pathological processes. We have previously reported that p130Cas supports cell migration through the binding to Src as well as phosphorylation-dependent association with actin retrograde flow at focal adhesions. However, it remains elusive how phosphorylated Cas interacts with actin cytoskeletons. We observe that the actin-binding protein, tensin 1, co-localizes with Cas, but not with its phosphorylation-defective mutant, at focal adhesions in leading regions of migrating cells. While a truncation mutant of tensin 1 that lacks the phosphotyrosine-binding PTB and SH2 domains (tensin 1-SH2PTB) poorly co-localizes or co-immunoprecitates with Cas, bacterially expressed recombinant tensin 1-SH2PTB protein binds to Casin vitroin a Cas phosphorylation-dependent manner. Furthermore, exogenous expression of tensin 1-SH2PTB, which is devoid of the actin-interacting motifs, interferes with the Cas-driven cell migration, slows down the inward flux of Cas molecules, and impedes the displacement of Cas molecules from focal adhesions. Taken together, our results show that tensin 1 links inwardly moving actin cytoskeletons to phosphorylated Cas at focal adhesions, thereby driving cell migration.
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Affiliation(s)
- Zhihai Zhao
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Song Hui Tan
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore Department of Biomedical Engineering, National University of Singapore, 9 Engineering Drive 1, Block EA, #03-12, 117575, Singapore
| | - Hiroaki Machiyama
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Keiko Kawauchi
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Keigo Araki
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Hiroaki Hirata
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
| | - Yasuhiro Sawada
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore Department of Biomedical Engineering, National University of Singapore, 9 Engineering Drive 1, Block EA, #03-12, 117575, Singapore Department of Rehabilitation for the Movement Functions, National Rehabilitation Center for Persons with Disabilities, 4-1 Namiki, Tokorozawa, Saitama 359-8555, Japan Laboratory for Mechanical Medicine, Locomotive Syndrome Research Institute, Nadogaya Hospital, 687-4 Nadogaya, Kashiwa, Chiba 277-0032, Japan
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59
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Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization. PLoS Genet 2016; 12:e1005885. [PMID: 26925779 PMCID: PMC4771162 DOI: 10.1371/journal.pgen.1005885] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 01/30/2016] [Indexed: 02/07/2023] Open
Abstract
Protein tyrosine kinases (PTKs) are a group of closely related enzymes that have evolutionarily diverged from serine/threonine kinases (STKs) to regulate pathways associated with multi-cellularity. Evolutionary divergence of PTKs from STKs has occurred through accumulation of mutations in the active site as well as in the commonly conserved hydrophobic core. While the functional significance of active site variations is well understood, relatively little is known about how hydrophobic core variations contribute to PTK evolutionary divergence. Here, using a combination of statistical sequence comparisons, molecular dynamics simulations, mutational analysis and in vitro thermostability and kinase assays, we investigate the structural and functional significance of key PTK-specific variations in the kinase core. We find that the nature of residues and interactions in the hydrophobic core of PTKs is strikingly different from other protein kinases, and PTK-specific variations in the core contribute to functional divergence by altering the stability and dynamics of the kinase domain. In particular, a functionally critical STK-conserved histidine that stabilizes the regulatory spine in STKs is selectively mutated to an alanine, serine or glutamate in PTKs, and this loss-of-function mutation is accommodated, in part, through compensatory PTK-specific interactions in the core. In particular, a PTK-conserved phenylalanine in the I-helix appears to structurally and functionally compensate for the loss of STK-histidine by interacting with the regulatory spine, which has far-reaching effects on enzyme activity, inhibitor sensing, and stability. We propose that hydrophobic core variations provide a selective advantage during PTK evolution by increasing the conformational flexibility, and therefore the allosteric potential of the kinase domain. Our studies also suggest that Tyrosine Kinase Like kinases such as RAF are intermediates in PTK evolutionary divergence inasmuch as they share features of both PTKs and STKs in the core. Finally, our studies provide an evolutionary framework for identifying and characterizing disease and drug resistance mutations in the kinase core. Proteins evolve new functions through accumulation of mutations in the primary sequence. Understanding how naturally occurring mutations shape protein function can provide insights into how non-natural mutations contribute to disease. Here, we identify sequence variants associated with the functional specialization of tyrosine kinases, a large and medically important class of proteins associated with the evolution of complex multicellular functions and diseases such as cancer. We find that mutations distal from the active site contribute to functional specialization by altering the stability, activity and dynamics of the kinase core. Our findings have implications for understanding the evolution of allosteric regulation in tyrosine kinases, and in predicting the structural and functional impact of disease and drug resistance mutations in the kinase core.
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Chapter Six - The Ubiquitin Network in the Control of EGFR Endocytosis and Signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:225-76. [DOI: 10.1016/bs.pmbts.2016.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Huang Z, Marsiglia WM, Basu Roy U, Rahimi N, Ilghari D, Wang H, Chen H, Gai W, Blais S, Neubert TA, Mansukhani A, Traaseth NJ, Li X, Mohammadi M. Two FGF Receptor Kinase Molecules Act in Concert to Recruit and Transphosphorylate Phospholipase Cγ. Mol Cell 2015; 61:98-110. [PMID: 26687682 DOI: 10.1016/j.molcel.2015.11.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/28/2015] [Accepted: 11/05/2015] [Indexed: 11/28/2022]
Abstract
The molecular basis by which receptor tyrosine kinases (RTKs) recruit and phosphorylate Src Homology 2 (SH2) domain-containing substrates has remained elusive. We used X-ray crystallography, NMR spectroscopy, and cell-based assays to demonstrate that recruitment and phosphorylation of Phospholipase Cγ (PLCγ), a prototypical SH2 containing substrate, by FGF receptors (FGFR) entails formation of an allosteric 2:1 FGFR-PLCγ complex. We show that the engagement of pTyr-binding pocket of the cSH2 domain of PLCγ by the phosphorylated tail of an FGFR kinase induces a conformational change at the region past the cSH2 core domain encompassing Tyr-771 and Tyr-783 to facilitate the binding/phosphorylation of these tyrosines by another FGFR kinase in trans. Our data overturn the current paradigm that recruitment and phosphorylation of substrates are carried out by the same RTK monomer in cis and disclose an obligatory role for receptor dimerization in substrate phosphorylation in addition to its canonical role in kinase activation.
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Affiliation(s)
- Zhifeng Huang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Upal Basu Roy
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Nader Rahimi
- Department of Pathology and Laboratory of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Dariush Ilghari
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Huiyan Wang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Huaibin Chen
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Weiming Gai
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Steven Blais
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Alka Mansukhani
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Xiaokun Li
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Moosa Mohammadi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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Thapa N, Choi S, Tan X, Wise T, Anderson RA. Phosphatidylinositol Phosphate 5-Kinase Iγ and Phosphoinositide 3-Kinase/Akt Signaling Couple to Promote Oncogenic Growth. J Biol Chem 2015; 290:18843-54. [PMID: 26070568 DOI: 10.1074/jbc.m114.596742] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 11/06/2022] Open
Abstract
The assembly of signaling complexes at the plasma membrane is required for the initiation and propagation of cellular signaling upon cell activation. The class I PI3K and the serine/threonine-specific protein kinase Akt signaling pathways (PI3K/Akt) are often activated in tumors. These pathways are initiated by the generation of phosphatidylinositol 3,4,5-triphosphate (PIP3) by PI3K-mediated phosphorylation of phosphatidylinositol 4,5-biphosphate (PIP2), synthesized by phosphatidylinositol 4-phosphate 5-kinase (PIPKI) enzymes. The mechanism of how tumor cells recruit and organize the PIP2-synthesizing enzymes with PI3K in the plasma membrane for activation of PI3K/Akt signaling is not defined. Here, we demonstrated a role for the phosphatidylinositol 4-phosphate 5-kinase Iγ (PIPKIγ) in PI3K/Akt signaling. PIPKIγ is overexpressed in triple-negative breast cancers. Loss of PIPKIγ or its focal adhesion-targeting variant, PIPKIγi2, impaired PI3K/Akt activation upon stimulation with growth factors or extracellular matrix proteins in different tumor cells. PIPKIγi2 assembles into a complex containing Src and PI3K; Src was required for the recruitment of PI3K enzyme into the complex. PIPKIγi2 interaction with Src and its lipid kinase activity were required for promoting PI3K/Akt signaling. These results define a mechanism by which PIPKIγi2 and PI3K are integrated into a complex regulated by Src, resulting in the spatial generation of PIP2, which is the substrate PI3K required for PIP3 generation and subsequent Akt activation. This study elucidates the mechanism by which PIP2-generating enzyme controls Akt activation upstream of a PI3K enzyme. This pathway may represent a signaling nexus required for the survival and growth of metastasizing and circulating tumor cells in vivo.
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Affiliation(s)
- Narendra Thapa
- From the Molecular and Cellular Pharmacology Program, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Suyong Choi
- From the Molecular and Cellular Pharmacology Program, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Xiaojun Tan
- From the Molecular and Cellular Pharmacology Program, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Thomas Wise
- From the Molecular and Cellular Pharmacology Program, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Richard A Anderson
- From the Molecular and Cellular Pharmacology Program, University of Wisconsin, School of Medicine and Public Health, Madison, Wisconsin 53706
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LASP1 is a novel BCR-ABL substrate and a phosphorylation-dependent binding partner of CRKL in chronic myeloid leukemia. Oncotarget 2015; 5:5257-71. [PMID: 24913448 PMCID: PMC4170624 DOI: 10.18632/oncotarget.2072] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by a genomic translocation generating a permanently active BCR-ABL oncogene with a complex pattern of atypically tyrosine-phosphorylated proteins that drive the malignant phenotype of CML. Recently, the LIM and SH3 domain protein 1 (LASP1) was identified as a component of a six gene signature that is strongly predictive for disease progression and relapse in CML patients. However, the underlying mechanisms why LASP1 expression correlates with dismal outcome remained unresolved. Here, we identified LASP1 as a novel and overexpressed direct substrate of BCR-ABL in CML. We demonstrate that LASP1 is specifically phosphorylated by BCR-ABL at tyrosine-171 in CML patients, which is abolished by tyrosine kinase inhibitor therapy. Further studies revealed that LASP1 phosphorylation results in an association with CRKL - another specific BCR-ABL substrate and bona fide biomarker for BCR-ABL activity. pLASP1-Y171 binds to non-phosphorylated CRKL at its SH2 domain. Accordingly, the BCR-ABL-mediated pathophysiological hyper-phosphorylation of LASP1 in CML disrupts normal regulation of CRKL and LASP1, which likely has implications on downstream BCR-ABL signaling. Collectively, our results suggest that LASP1 phosphorylation might serve as an additional candidate biomarker for assessment of BCR-ABL activity and provide a first step toward a molecular understanding of LASP1 function in CML.
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Abstract
Prolactin is a hormone that is mainly secreted by lactotroph cells of the anterior pituitary gland, and is involved in many biological processes including lactation and reproduction. Animal models have provided insights into the biology of prolactin proteins and offer compelling evidence that the different prolactin isoforms each have independent biological functions. The major isoform, 23 kDa prolactin, acts via its membrane receptor, the prolactin receptor (PRL-R), which is a member of the haematopoietic cytokine superfamily and for which the mechanism of activation has been deciphered. The 16 kDa prolactin isoform is a cleavage product derived from native prolactin, which has received particular attention as a result of its newly described inhibitory effects on angiogenesis and tumorigenesis. The discovery of multiple extrapituitary sites of prolactin secretion also increases the range of known functions of this hormone. This Review summarizes current knowledge of the biology of prolactin and its receptor, as well as its physiological and pathological roles. We focus on the role of prolactin in human pathophysiology, particularly the discovery of the mechanism underlying infertility associated with hyperprolactinaemia and the identification of the first mutation in human PRLR.
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Affiliation(s)
- Valérie Bernard
- Inserm U1185, 63 rue Gabriel Péri, 94276 Le Kremlin-Bicêtre Cedex, France
| | - Jacques Young
- Hôpital Bicêtre, Service d'Endocrinologie et des Maladies de la Reproduction, 78 rue du Général Leclerc 94275 Le Kremlin-Bicêtre Cedex, France
| | - Philippe Chanson
- Hôpital Bicêtre, Service d'Endocrinologie et des Maladies de la Reproduction, 78 rue du Général Leclerc 94275 Le Kremlin-Bicêtre Cedex, France
| | - Nadine Binart
- Inserm U1185, 63 rue Gabriel Péri, 94276 Le Kremlin-Bicêtre Cedex, France
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65
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Azuaje F, Tiemann K, Niclou SP. Therapeutic control and resistance of the EGFR-driven signaling network in glioblastoma. Cell Commun Signal 2015; 13:23. [PMID: 25885672 PMCID: PMC4391485 DOI: 10.1186/s12964-015-0098-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 03/10/2015] [Indexed: 12/31/2022] Open
Abstract
The alteration of the epidermal growth factor receptor (EGFR)-driven signaling network is a characteristic feature of glioblastomas (GBM), and its inhibition represents a treatment strategy. However, EGFR-targeted interventions have been largely ineffective. Complex perturbations in this system are likely to be central to tumor cells with high adaptive capacity and resistance to therapies. We review key concepts and mechanisms relevant to EGFR-targeted treatment resistance at a systems level. Our understanding of treatment resistance as a systems-level phenomenon is necessary to develop effective therapeutic options for GBM patients. This is allowing us to go beyond the notion of therapeutic targets as single molecular components, into strategies that can weaken cancer signaling robustness and boost inherent network-level vulnerabilities.
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Affiliation(s)
- Francisco Azuaje
- Department of Oncology, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.
| | - Katja Tiemann
- Department of Oncology, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.
| | - Simone P Niclou
- Department of Oncology, NorLux Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg.
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66
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Grossmann A, Benlasfer N, Birth P, Hegele A, Wachsmuth F, Apelt L, Stelzl U. Phospho-tyrosine dependent protein-protein interaction network. Mol Syst Biol 2015; 11:794. [PMID: 25814554 PMCID: PMC4380928 DOI: 10.15252/msb.20145968] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Post-translational protein modifications, such as tyrosine phosphorylation, regulate protein–protein interactions (PPIs) critical for signal processing and cellular phenotypes. We extended an established yeast two-hybrid system employing human protein kinases for the analyses of phospho-tyrosine (pY)-dependent PPIs in a direct experimental, large-scale approach. We identified 292 mostly novel pY-dependent PPIs which showed high specificity with respect to kinases and interacting proteins and validated a large fraction in co-immunoprecipitation experiments from mammalian cells. About one-sixth of the interactions are mediated by known linear sequence binding motifs while the majority of pY-PPIs are mediated by other linear epitopes or governed by alternative recognition modes. Network analysis revealed that pY-mediated recognition events are tied to a highly connected protein module dedicated to signaling and cell growth pathways related to cancer. Using binding assays, protein complementation and phenotypic readouts to characterize the pY-dependent interactions of TSPAN2 (tetraspanin 2) and GRB2 or PIK3R3 (p55γ), we exemplarily provide evidence that the two pY-dependent PPIs dictate cellular cancer phenotypes.
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Affiliation(s)
- Arndt Grossmann
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Nouhad Benlasfer
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Petra Birth
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Anna Hegele
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Franziska Wachsmuth
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Luise Apelt
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Ulrich Stelzl
- Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
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67
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Huang Z, Tan L, Wang H, Liu Y, Blais S, Deng J, Neubert TA, Gray NS, Li X, Mohammadi M. DFG-out mode of inhibition by an irreversible type-1 inhibitor capable of overcoming gate-keeper mutations in FGF receptors. ACS Chem Biol 2015; 10:299-309. [PMID: 25317566 PMCID: PMC4301177 DOI: 10.1021/cb500674s] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Drug-resistance
acquisition through kinase gate-keeper mutations is a major hurdle
in the clinic. Here, we determined the first crystal structures of
the human FGFR4 kinase domain (FGFR4K) alone and complexed with ponatinib,
a promiscuous type-2 (DFG-out) kinase inhibitor, and an oncogenic
FGFR4K harboring the V550L gate-keeper mutation bound to FIIN-2, a
new type-1 irreversible inhibitor. Remarkably, like ponatinib, FIIN-2
also binds in the DFG-out mode despite lacking a functional group
necessary to occupy the pocket vacated upon the DFG-out flip. Structural
analysis reveals that the covalent bond between FIIN-2 and a cysteine,
uniquely present in the glycine-rich loop of FGFR kinases, facilitates
the DFG-out conformation, which together with the internal flexibility
of FIIN-2 enables FIIN-2 to avoid the steric clash with the gate-keeper
mutation that causes the ponatinib resistance. The structural data
provide a blueprint for the development of next generation anticancer
inhibitors through combining the salient inhibitory mechanisms of
ponatinib and FIIN-2.
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Affiliation(s)
- Zhifeng Huang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Li Tan
- Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Huiyan Wang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | | | | | | | | | - Nathanael S. Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xiaokun Li
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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68
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Wang W, Xu S, Yin M, Jin ZG. Essential roles of Gab1 tyrosine phosphorylation in growth factor-mediated signaling and angiogenesis. Int J Cardiol 2014; 181:180-4. [PMID: 25528308 DOI: 10.1016/j.ijcard.2014.10.148] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 09/08/2014] [Accepted: 10/18/2014] [Indexed: 12/16/2022]
Abstract
Growth factors and their downstream receptor tyrosine kinases (RTKs) mediate a number of biological processes controlling cell function. Adaptor (docking) proteins, which consist exclusively of domains and motifs that mediate molecular interactions, link receptor activation to downstream effectors. Recent studies have revealed that Grb2-associated-binders (Gab) family members (including Gab1, Gab2, and Gab3), when phosphorylated on tyrosine residues, provide binding sites for multiple effector proteins, such as Src homology-2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2) and phosphatidylinositol 3-kinase (PI3K) regulatory subunit p85, thereby playing important roles in transducing RTKs-mediated signals into pathways with diversified biological functions. Here, we provide an up-to-date overview on the domain structure and biological functions of Gab1, the most intensively studied Gab family protein, in growth factor signaling and biological functions, with a special focus on angiogenesis.
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Affiliation(s)
- Weiye Wang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Suowen Xu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Meimei Yin
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Zheng Gen Jin
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA.
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69
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Gray EJ, Petsalaki E, James DA, Bagshaw RD, Stacey MM, Rocks O, Gingras AC, Pawson T. Src homology 2 domain containing protein 5 (SH2D5) binds the breakpoint cluster region protein, BCR, and regulates levels of Rac1-GTP. J Biol Chem 2014; 289:35397-408. [PMID: 25331951 DOI: 10.1074/jbc.m114.615112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SH2D5 is a mammalian-specific, uncharacterized adaptor-like protein that contains an N-terminal phosphotyrosine-binding domain and a C-terminal Src homology 2 (SH2) domain. We show that SH2D5 is highly enriched in adult mouse brain, particularly in Purkinjie cells in the cerebellum and the cornu ammonis of the hippocampus. Despite harboring two potential phosphotyrosine (Tyr(P)) recognition domains, SH2D5 binds minimally to Tyr(P) ligands, consistent with the absence of a conserved Tyr(P)-binding arginine residue in the SH2 domain. Immunoprecipitation coupled to mass spectrometry (IP-MS) from cultured cells revealed a prominent association of SH2D5 with breakpoint cluster region protein, a RacGAP that is also highly expressed in brain. This interaction occurred between the phosphotyrosine-binding domain of SH2D5 and an NxxF motif located within the N-terminal region of the breakpoint cluster region. siRNA-mediated depletion of SH2D5 in a neuroblastoma cell line, B35, induced a cell rounding phenotype correlated with low levels of activated Rac1-GTP, suggesting that SH2D5 affects Rac1-GTP levels. Taken together, our data provide the first characterization of the SH2D5 signaling protein.
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Affiliation(s)
- Elizabeth J Gray
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada,
| | - Evangelia Petsalaki
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - D Andrew James
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada, Sanofi Pasteur, Toronto, Ontario M2R3T4, Canada, and
| | - Richard D Bagshaw
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Melissa M Stacey
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
| | - Oliver Rocks
- the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada, the Max Delbrück Center for Molecular Medicine Berlin-Buch, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Anne-Claude Gingras
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada,
| | - Tony Pawson
- From the Department of Molecular Genetics, University of Toronto, Ontario M5S1A8, Canada, the Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G1X5, Canada
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70
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Chou RH, Wang YN, Hsieh YH, Li LY, Xia W, Chang WC, Chang LC, Cheng CC, Lai CC, Hsu JL, Chang WJ, Chiang SY, Lee HJ, Liao HW, Chuang PH, Chen HY, Wang HL, Kuo SC, Chen CH, Yu YL, Hung MC. EGFR modulates DNA synthesis and repair through Tyr phosphorylation of histone H4. Dev Cell 2014; 30:224-37. [PMID: 25073158 DOI: 10.1016/j.devcel.2014.06.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 03/21/2014] [Accepted: 06/05/2014] [Indexed: 12/17/2022]
Abstract
Posttranslational modifications of histones play fundamental roles in many biological functions. Specifically, histone H4-K20 methylation is critical for DNA synthesis and repair. However, little is known about how these functions are regulated by the upstream stimuli. Here, we identify a tyrosine phosphorylation site at Y72 of histone H4, which facilitates recruitment of histone methyltransferases (HMTases), SET8 and SUV4-20H, to enhance its K20 methylation, thereby promoting DNA synthesis and repair. Phosphorylation-defective histone H4 mutant is deficient in K20 methylation, leading to reduced DNA synthesis, delayed cell cycle progression, and decreased DNA repair ability. Disrupting the interaction between epidermal growth factor receptor (EGFR) and histone H4 by Y72 peptide significantly reduced tumor growth. Furthermore, EGFR expression clinically correlates with histone H4-Y72 phosphorylation, H4-K20 monomethylation, and the Ki-67 proliferation marker. These findings uncover a mechanism by which EGFR transduces signal to chromatin to regulate DNA synthesis and repair.
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Affiliation(s)
- Ruey-Hwang Chou
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan; Department of Biotechnology, Asia University, Taichung 413, Taiwan
| | - Ying-Nai Wang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yi-Hsien Hsieh
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Long-Yuan Li
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan; Department of Biotechnology, Asia University, Taichung 413, Taiwan
| | - Weiya Xia
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei-Chao Chang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ling-Chu Chang
- Graduate Institute of Pharmaceutical Chemical, China Medical University, Taichung 404, Taiwan
| | - Chien-Chia Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chien-Chen Lai
- Graduate Institute of Chinese Medical Science, China Medical University and Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
| | - Jennifer L Hsu
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei-Jung Chang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Shu-Ya Chiang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Hong-Jen Lee
- Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hsin-Wei Liao
- Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pei-Huan Chuang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Hui-Yu Chen
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Hung-Ling Wang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan
| | - Sheng-Chu Kuo
- Graduate Institute of Pharmaceutical Chemical, China Medical University, Taichung 404, Taiwan
| | | | - Yung-Luen Yu
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan; Department of Biotechnology, Asia University, Taichung 413, Taiwan.
| | - Mien-Chie Hung
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan; Department of Biotechnology, Asia University, Taichung 413, Taiwan; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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71
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Hybrid and rogue kinases encoded in the genomes of model eukaryotes. PLoS One 2014; 9:e107956. [PMID: 25255313 PMCID: PMC4177888 DOI: 10.1371/journal.pone.0107956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/18/2014] [Indexed: 11/19/2022] Open
Abstract
The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes-S.cerevisiae, D. melanogaster, C.elegans, M.musculus, T.rubripes and H.sapiens-and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P.falciparum sheds light on possible strategies in host-pathogen interactions.
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72
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Lin C, Ear J, Midde K, Lopez-Sanchez I, Aznar N, Garcia-Marcos M, Kufareva I, Abagyan R, Ghosh P. Structural basis for activation of trimeric Gi proteins by multiple growth factor receptors via GIV/Girdin. Mol Biol Cell 2014; 25:3654-71. [PMID: 25187647 PMCID: PMC4230624 DOI: 10.1091/mbc.e14-05-0978] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
GIV, a guanidine exchange factor for trimeric Gi, contains a unique domain that functions like a SH2 domain. GIV's SH2-like domain binds autophosphorylated RTKs. Binding of GIV's SH2 to RTKs enables the receptors to activate trimeric Gi. Inhibition of GIV:RTK interaction abolishes GIV-dependent Akt enhancement downstream of RTKs. A long-standing issue in the field of signal transduction is to understand the cross-talk between receptor tyrosine kinases (RTKs) and heterotrimeric G proteins, two major and distinct signaling hubs that control eukaryotic cell behavior. Although stimulation of many RTKs leads to activation of trimeric G proteins, the molecular mechanisms behind this phenomenon remain elusive. We discovered a unifying mechanism that allows GIV/Girdin, a bona fide metastasis-related protein and a guanine-nucleotide exchange factor (GEF) for Gαi, to serve as a direct platform for multiple RTKs to activate Gαi proteins. Using a combination of homology modeling, protein–protein interaction, and kinase assays, we demonstrate that a stretch of ∼110 amino acids within GIV C-terminus displays structural plasticity that allows folding into a SH2-like domain in the presence of phosphotyrosine ligands. Using protein–protein interaction assays, we demonstrated that both SH2 and GEF domains of GIV are required for the formation of a ligand-activated ternary complex between GIV, Gαi, and growth factor receptors and for activation of Gαi after growth factor stimulation. Expression of a SH2-deficient GIV mutant (Arg 1745→Leu) that cannot bind RTKs impaired all previously demonstrated functions of GIV—Akt enhancement, actin remodeling, and cell migration. The mechanistic and structural insights gained here shed light on the long-standing questions surrounding RTK/G protein cross-talk, set a novel paradigm, and characterize a unique pharmacological target for uncoupling GIV-dependent signaling downstream of multiple oncogenic RTKs.
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Affiliation(s)
- Changsheng Lin
- Department of Medicine, University of California, San Diego, School of Medicine, CA 92093
| | - Jason Ear
- Department of Medicine, University of California, San Diego, School of Medicine, CA 92093
| | - Krishna Midde
- Department of Medicine, University of California, San Diego, School of Medicine, CA 92093
| | | | - Nicolas Aznar
- Department of Medicine, University of California, San Diego, School of Medicine, CA 92093
| | - Mikel Garcia-Marcos
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, CA 92093
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Pradipta Ghosh
- Department of Medicine, University of California, San Diego, School of Medicine, CA 92093
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73
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McAllister TE, Horner KA, Webb ME. Evaluation of the interaction between phosphohistidine analogues and phosphotyrosine binding domains. Chembiochem 2014; 15:1088-91. [PMID: 24771713 PMCID: PMC4159583 DOI: 10.1002/cbic.201402090] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 12/16/2022]
Abstract
We have investigated the interaction of peptides containing phosphohistidine analogues and their homologues with the prototypical phosphotyrosine binding SH2 domain from the eukaryotic cell signalling protein Grb2 by using a combination of isothermal titration calorimetry and a fluorescence anisotropy competition assay. These investigations demonstrated that the triazole class of phosphohistidine analogues are capable of binding too, suggesting that phosphohistidine could potentially be detected by this class of proteins in vivo.
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Affiliation(s)
- Tom E McAllister
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
| | - Katherine A Horner
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
| | - Michael E Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of LeedsWoodhouse Lane, Leeds, LS2 9JT (UK) E-mail: Homepage: http://www.chem.leeds.ac.uk/MEW/
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74
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Borthakur S, Lee H, Kim S, Wang BC, Buck M. Binding and function of phosphotyrosines of the Ephrin A2 (EphA2) receptor using synthetic sterile α motif (SAM) domains. J Biol Chem 2014; 289:19694-703. [PMID: 24825902 DOI: 10.1074/jbc.m114.567602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The sterile α motif (SAM) domain of the ephrin receptor tyrosine kinase, EphA2, undergoes tyrosine phosphorylation, but the effect of phosphorylation on the structure and interactions of the receptor is unknown. Studies to address these questions have been hindered by the difficulty of obtaining site-specifically phosphorylated proteins in adequate amounts. Here, we describe the use of chemically synthesized and specifically modified domain-length peptides to study the behavior of phosphorylated EphA2 SAM domains. We show that tyrosine phosphorylation of any of the three tyrosines, Tyr(921), Tyr(930), and Tyr(960), has a surprisingly small effect on the EphA2 SAM structure and stability. However, phosphorylation at Tyr(921) and Tyr(930) enables differential binding to the Src homology 2 domain of the adaptor protein Grb7, which we propose will lead to distinct functional outcomes. Setting up different signaling platforms defined by selective interactions with adaptor proteins thus adds another level of regulation to EphA2 signaling.
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Affiliation(s)
| | - HyeongJu Lee
- From the Departments of Physiology and Biophysics
| | | | - Bing-Cheng Wang
- From the Departments of Physiology and Biophysics, Pharmacology, and the Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, Ohio 44109the Case Comprehensive Cancer Center, and
| | - Matthias Buck
- From the Departments of Physiology and Biophysics, the Case Comprehensive Cancer Center, and Neurosciences, the Case Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106 and
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75
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Chakraborty S, Umasankar PK, Preston GM, Khandelwal P, Apodaca G, Watkins SC, Traub LM. A phosphotyrosine switch for cargo sequestration at clathrin-coated buds. J Biol Chem 2014; 289:17497-514. [PMID: 24798335 DOI: 10.1074/jbc.m114.556589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The AP-2 clathrin adaptor complex oversees endocytic cargo selection in two parallel but independent manners. First, by physically engaging peptide-based endocytic sorting signals, a subset of clathrin-dependent transmembrane cargo is directly collected into assembling buds. Synchronously, by interacting with an assortment of clathrin-associated sorting proteins (CLASPs) that independently select different integral membrane cargo for inclusion within the incipient bud, AP-2 handles additional cargo capture indirectly. The distal platform subdomain of the AP-2 β2 subunit appendage is a privileged CLASP-binding surface that recognizes a cognate, short α-helical interaction motif. This signal, found in the CLASPs β-arrestin and the autosomal recessive hypercholesterolemia (ARH) protein, docks into an elongated groove on the β2 appendage platform. Tyr-888 is a critical constituent of this spatially confined β2 appendage contact interface and is phosphorylated in numerous high-throughput proteomic studies. We find that a phosphomimetic Y888E substitution does not interfere with incorporation of expressed β2-YFP subunit into AP-2 or alter AP-2 deposition at surface clathrin-coated structures. The Y888E mutation does not affect interactions involving the sandwich subdomain of the β2 appendage, indicating that the mutated appendage is folded and operational. However, the Y888E, but not Y888F, switch selectively uncouples interactions with ARH and β-arrestin. Phyogenetic conservation of Tyr-888 suggests that this residue can reversibly control occupancy of the β2 platform-binding site and, hence, cargo sorting.
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Affiliation(s)
| | | | | | - Puneet Khandelwal
- the Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Gerard Apodaca
- the Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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76
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Gower CM, Chang MEK, Maly DJ. Bivalent inhibitors of protein kinases. Crit Rev Biochem Mol Biol 2014; 49:102-15. [PMID: 24564382 DOI: 10.3109/10409238.2013.875513] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein kinases are key players in a large number of cellular signaling pathways. Dysregulated kinase activity has been implicated in a number of diseases, and members of this enzyme family are of therapeutic interest. However, due to the fact that most inhibitors interact with the highly conserved ATP-binding sites of kinases, it is a significant challenge to develop pharmacological agents that target only one of the greater than 500 kinases present in humans. A potential solution to this problem is the development of bisubstrate and bivalent kinase inhibitors, in which an active site-directed moiety is tethered to another ligand that targets a location outside of the ATP-binding cleft. Because kinase signaling specificity is modulated by regions outside of the ATP-binding site, strategies that exploit these interactions have the potential to provide reagents with high target selectivity. This review highlights examples of kinase interaction sites that can potentially be exploited by bisubstrate and bivalent inhibitors. Furthermore, an overview of efforts to target these interactions with bisubstrate and bivalent inhibitors is provided. Finally, several examples of the successful application of these reagents in a cellular setting are described.
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Affiliation(s)
- Carrie M Gower
- Department of Chemistry, University of Washington , Seattle, WA , USA
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77
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Clinical targeting of mutated and wild-type protein tyrosine kinases in cancer. Mol Cell Biol 2014; 34:1722-32. [PMID: 24567371 DOI: 10.1128/mcb.01592-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Clinical therapies for cancer have evolved from toxic, nontargeted agents to manageable, highly targeted therapies. Protein tyrosine kinases are a family of signaling molecules implicated in nearly every cancer type and are the foundation for the development of modern targeted agents. Recent genomic analyses have identified activating mutations, translocations, and amplifications of tyrosine kinases. Selective targeting of these genetically altered tyrosine kinases has resulted in significant clinical advances, including increased patient survival. This indicates that altered protein tyrosine kinases are the main drivers of many different cancers. However, lost during analyses of genetic lesions are the contributions of activated, wild-type kinases on tumor-dependent pathways. New approaches in phosphoproteomic technologies have identified several wild-type tyrosine kinase activation states, suggesting that non-genetically altered kinases can be essential "nodes" for signal transduction. Here, we summarize the evidence supporting the common mechanisms of protein tyrosine kinase activation in cancer and provide a personal perspective on the kinases BCR-ABL and BTK, as well as nonmutated kinase targets in prostate cancer, through our work. We outline the mechanisms of tyrosine kinase activation in the absence of direct mutation and discuss whether non-genetically altered tyrosine kinases or their associated downstream signaling pathways can be effectively targeted.
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78
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Ohashi K, Sampei K, Nakagawa M, Uchiumi N, Amanuma T, Aiba S, Oikawa M, Mizuno K. Damnacanthal, an effective inhibitor of LIM-kinase, inhibits cell migration and invasion. Mol Biol Cell 2014; 25:828-40. [PMID: 24478456 PMCID: PMC3952852 DOI: 10.1091/mbc.e13-09-0540] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Damnacanthal is identified as an effective inhibitor of LIM-kinase. It inhibits chemotaxis of T-cells and migration and invasion of breast carcinoma cells in culture and hapten-induced migration of epidermal Langerhans cells in mouse ears. Damnacanthal is a useful tool for investigating the cellular and physiological functions of LIM-kinase. LIM-kinases (LIMKs) play crucial roles in various cell activities, including migration, division, and morphogenesis, by phosphorylating and inactivating cofilin. Using a bimolecular fluorescence complementation assay to detect the actin–cofilin interaction, we screened LIMK1 inhibitors and identified two effective inhibitors, damnacanthal (Dam) and MO-26 (a pyrazolopyrimidine derivative). These compounds have already been shown to inhibit Lck, a Src family tyrosine kinase. However, in vitro kinase assays revealed that Dam inhibited LIMK1 more effectively than Lck. Dam suppressed LIMK1-induced cofilin phosphorylation and deceleration of actin retrograde flow in lamellipodia in N1E-115 cells. Dam impaired CXCL12-induced chemotactic migration of Jurkat T lymphocytes and Jurkat-derived, Lck-deficient JCaM1.6 cells and also inhibited serum-induced migration and invasion of MDA-MB-231 breast carcinoma cells. These results suggest that Dam has the potential to suppress cell migration and invasion primarily through the inhibition of LIMK kinase activity. Topical application of Dam also suppressed hapten-induced migration of epidermal Langerhans cells in mouse ears. Dam provides a useful tool for investigating cellular and physiological functions of LIMKs and holds promise for the development of agents against LIMK-related diseases. The bimolecular fluorescence complementation assay system used in this study will provide a useful method to screen for inhibitors of various protein kinases.
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Affiliation(s)
- Kazumasa Ohashi
- Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8574, Japan Graduate School of Nanobioscience, Yokohama City University, Seto, Kanazawa-ku, Yokohama 236-0027, Japan
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79
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Mehta S, Zhang J. Using a kinase-inducible bimolecular switch to control enzyme activity in living cells. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2014; 5:227-37. [PMID: 24391085 DOI: 10.1002/9780470559277.ch130090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular switches have been instrumental in the development of powerful and versatile genetic tools for directly probing biochemical processes, such as intracellular signaling, within their native contexts. A molecular switch can be broadly defined as a molecular system capable of existing in either of two states (e.g., conformations), which can be converted from one state to the other by a specific input stimulus. This protocol outlines a method for using a kinase-inducible bimolecular switch, along with live-cell fluorescence microscopy, to directly control and monitor the activity of a specific enzyme in living cells.
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Affiliation(s)
- Sohum Mehta
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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80
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Molecular mechanisms of SH2- and PTB-domain-containing proteins in receptor tyrosine kinase signaling. Cold Spring Harb Perspect Biol 2013; 5:a008987. [PMID: 24296166 DOI: 10.1101/cshperspect.a008987] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Intracellular signaling is mediated by reversible posttranslational modifications (PTMs) that include phosphorylation, ubiquitination, and acetylation, among others. In response to extracellular stimuli such as growth factors, receptor tyrosine kinases (RTKs) typically dimerize and initiate signaling through phosphorylation of their cytoplasmic tails and downstream scaffolds. Signaling effectors are recruited to these phosphotyrosine (pTyr) sites primarily through Src homology 2 (SH2) domains and pTyr-binding (PTB) domains. This review describes how these conserved domains specifically recognize pTyr residues and play a major role in mediating precise downstream signaling events.
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81
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Ruan GX, Kazlauskas A. Lactate engages receptor tyrosine kinases Axl, Tie2, and vascular endothelial growth factor receptor 2 to activate phosphoinositide 3-kinase/Akt and promote angiogenesis. J Biol Chem 2013; 288:21161-21172. [PMID: 23754286 DOI: 10.1074/jbc.m113.474619] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although a high level of lactate is quintessential to both tumors and wound healing, the manner by which lactate impacts endothelial cells to promote angiogenesis and thereby create or restore vascular perfusion to growing tissues has not been fully elucidated. Here we report that lactate activated the PI3K/Akt pathway in primary human endothelial cells. Furthermore, activating this signaling pathway was required for lactate-stimulated organization of endothelial cells into tubes and for sprouting of vessels from mouse aortic explants. Lactate engaged the PI3K/Akt pathway via ligand-mediated activation of the three receptor tyrosine kinases Axl, Tie2, and VEGF receptor 2. Neutralizing the ligands for these receptor tyrosine kinases, pharmacologically inhibiting their kinase activity or suppressing their expression largely eliminated the ability of cells and explants to respond to lactate. Elucidating the mechanism by which lactate communicates with endothelial cells presents a previously unappreciated opportunity to improve our understanding of the angiogenic program and to govern it.
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Affiliation(s)
- Guo-Xiang Ruan
- From the Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114
| | - Andrius Kazlauskas
- From the Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114.
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82
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Kundu K, Costa F, Huber M, Reth M, Backofen R. Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PLoS One 2013; 8:e62732. [PMID: 23690949 PMCID: PMC3656881 DOI: 10.1371/journal.pone.0062732] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/22/2013] [Indexed: 01/08/2023] Open
Abstract
Src homology 2 (SH2) domains are the largest family of the peptide-recognition modules (PRMs) that bind to phosphotyrosine containing peptides. Knowledge about binding partners of SH2-domains is key for a deeper understanding of different cellular processes. Given the high binding specificity of SH2, in-silico ligand peptide prediction is of great interest. Currently however, only a few approaches have been published for the prediction of SH2-peptide interactions. Their main shortcomings range from limited coverage, to restrictive modeling assumptions (they are mainly based on position specific scoring matrices and do not take into consideration complex amino acids inter-dependencies) and high computational complexity. We propose a simple yet effective machine learning approach for a large set of known human SH2 domains. We used comprehensive data from micro-array and peptide-array experiments on 51 human SH2 domains. In order to deal with the high data imbalance problem and the high signal-to-noise ration, we casted the problem in a semi-supervised setting. We report competitive predictive performance w.r.t. state-of-the-art. Specifically we obtain 0.83 AUC ROC and 0.93 AUC PR in comparison to 0.71 AUC ROC and 0.87 AUC PR previously achieved by the position specific scoring matrices (PSSMs) based SMALI approach. Our work provides three main contributions. First, we showed that better models can be obtained when the information on the non-interacting peptides (negative examples) is also used. Second, we improve performance when considering high order correlations between the ligand positions employing regularization techniques to effectively avoid overfitting issues. Third, we developed an approach to tackle the data imbalance problem using a semi-supervised strategy. Finally, we performed a genome-wide prediction of human SH2-peptide binding, uncovering several findings of biological relevance. We make our models and genome-wide predictions, for all the 51 SH2-domains, freely available to the scientific community under the following URLs: http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/SH2PepInt.tar.gz and http://www.bioinf.uni-freiburg.de/Software/SH2PepInt/Genome-wide-predictions.tar.gz, respectively.
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Affiliation(s)
- Kousik Kundu
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
| | - Fabrizio Costa
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Michael Huber
- Institute of Biochemistry and Molecular Immunology, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Michael Reth
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Department of Molecular Immunology, Max Planck Institute of Immunology, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
- Centre for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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83
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Posttranslational protein knockdown coupled to receptor tyrosine kinase activation with phosphoPROTACs. Proc Natl Acad Sci U S A 2013; 110:8942-7. [PMID: 23674677 DOI: 10.1073/pnas.1217206110] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Posttranslational knockdown of a specific protein is an attractive approach for examining its function within a system. Here we introduce phospho-dependent proteolysis targeting chimeras (phosphoPROTACs), a method to couple the conditional degradation of targeted proteins to the activation state of particular kinase-signaling pathways. We generated two phosphoPROTACs that couple the tyrosine phosphorylation sequences of either the nerve growth factor receptor, TrkA (tropomyosin receptor kinase A), or the neuregulin receptor, ErbB3 (erythroblastosis oncogene B3), with a peptide ligand for the E3 ubiquitin ligase von Hippel Lindau protein. These phosphoPROTACs recruit either the neurotrophic signaling effector fibroblast growth factor receptor substrate 2α or the survival-promoting phosphatidylinositol-3-kinase, respectively, to be ubiquitinated and degraded upon activation of specific receptor tyrosine kinases and phosphorylation of the phosphoPROTACs. We demonstrate the ability of these phosphoPROTACs to suppress the short- and long-term effects of their respective activating receptor tyrosine kinase pathways both in vitro and in vivo. In addition, we show that activation of phosphoPROTACs is entirely dependent on their kinase-mediated phosphorylation, as phenylalanine-containing null variants are inactive. Furthermore, stimulation of unrelated growth factor receptors does not induce target protein knockdown. Although comparable in efficiency to RNAi, this approach has the added advantage of providing a degree of temporal and dosing control as well as cell-type selectivity unavailable using nucleic acid-based strategies. By varying the autophosphorylation sequence of a phosphoPROTAC, it is conceivable that other receptor tyrosine kinase/effector pairings could be similarly exploited to achieve other biological effects.
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84
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Tanaka H, Akagi KI, Oneyama C, Tanaka M, Sasaki Y, Kanou T, Lee YH, Yokogawa D, Dobenecker MW, Nakagawa A, Okada M, Ikegami T. Identification of a new interaction mode between the Src homology 2 domain of C-terminal Src kinase (Csk) and Csk-binding protein/phosphoprotein associated with glycosphingolipid microdomains. J Biol Chem 2013; 288:15240-54. [PMID: 23548896 DOI: 10.1074/jbc.m112.439075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins with Src homology 2 (SH2) domains play major roles in tyrosine kinase signaling. Structures of many SH2 domains have been studied, and the regions involved in their interactions with ligands have been elucidated. However, these analyses have been performed using short peptides consisting of phosphotyrosine followed by a few amino acids, which are described as the canonical recognition sites. Here, we report the solution structure of the SH2 domain of C-terminal Src kinase (Csk) in complex with a longer phosphopeptide from the Csk-binding protein (Cbp). This structure, together with biochemical experiments, revealed the existence of a novel binding region in addition to the canonical phosphotyrosine 314-binding site of Cbp. Mutational analysis of this second region in cells showed that both canonical and novel binding sites are required for tumor suppression through the Cbp-Csk interaction. Furthermore, the data indicate an allosteric connection between Cbp binding and Csk activation that arises from residues in the βB/βC loop of the SH2 domain.
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Affiliation(s)
- Hiroaki Tanaka
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
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85
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Tsushima H, Malabarba MG, Confalonieri S, Senic-Matuglia F, Verhoef LGGC, Bartocci C, D'Ario G, Cocito A, Di Fiore PP, Salcini AE. A snapshot of the physical and functional wiring of the Eps15 homology domain network in the nematode. PLoS One 2013; 8:e56383. [PMID: 23424658 PMCID: PMC3570524 DOI: 10.1371/journal.pone.0056383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 01/13/2013] [Indexed: 12/12/2022] Open
Abstract
Protein interaction modules coordinate the connections within and the activity of intracellular signaling networks. The Eps15 Homology (EH) module, a protein-protein interaction domain that is a key feature of the EH-network, was originally identified in a few proteins involved in endocytosis and vesicle trafficking, and has subsequently also been implicated in actin reorganization, nuclear shuttling, and DNA repair. Here we report an extensive characterization of the physical connections and of the functional wirings of the EH-network in the nematode. Our data show that one of the major physiological roles of the EH-network is in neurotransmission. In addition, we found that the proteins of the network intersect, and possibly coordinate, a number of “territories” of cellular activity including endocytosis/recycling/vesicle transport, actin dynamics, general metabolism and signal transduction, ubiquitination/degradation of proteins, DNA replication/repair, and miRNA biogenesis and processing.
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Affiliation(s)
- Hanako Tsushima
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Maria Grazia Malabarba
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Dipartimento di Medicina, Chirurgia ed Odontoiatria, Università degli Studi di Milano, Milan, Italy
| | | | | | | | - Cristina Bartocci
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Giovanni D'Ario
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Andrea Cocito
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Pier Paolo Di Fiore
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Dipartimento di Medicina, Chirurgia ed Odontoiatria, Università degli Studi di Milano, Milan, Italy
- Istituto Europeo di Oncologia, Milan, Italy
- * E-mail: (PPDF); (AES)
| | - Anna Elisabetta Salcini
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- * E-mail: (PPDF); (AES)
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86
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Krishnan H, Miller WT, Goldberg GS. SRC points the way to biomarkers and chemotherapeutic targets. Genes Cancer 2012; 3:426-35. [PMID: 23226580 DOI: 10.1177/1947601912458583] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The role of Src in tumorigenesis has been extensively studied since the work of Peyton Rous over a hundred years ago. Src is a non-receptor tyrosine kinase that plays key roles in signaling pathways controlling tumor cell growth and migration. Src regulates the activities of numerous molecules to induce cell transformation. However, transformed cells do not always migrate and realize their tumorigenic potential. They can be normalized by surrounding nontransformed cells by a process called contact normalization. Tumor cells need to override contact normalization to become malignant or metastatic. In this review, we discuss the role of Src in cell migration and contact normalization, with emphasis on Cas and Abl pathways. This paradigm illuminates several chemotherapeutic targets and may lead to the identification of new biomarkers and the development of effective anticancer treatments.
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Affiliation(s)
- Harini Krishnan
- University of Medicine and Dentistry of New Jersey, Graduate School of Biomedical Sciences, School of Osteopathic Medicine, Stratford, NJ, USA
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87
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Evans JV, Ammer AG, Jett JE, Bolcato CA, Breaux JC, Martin KH, Culp MV, Gannett PM, Weed SA. Src binds cortactin through an SH2 domain cystine-mediated linkage. J Cell Sci 2012; 125:6185-97. [PMID: 23097045 DOI: 10.1242/jcs.121046] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Tyrosine-kinase-based signal transduction mediated by modular protein domains is critical for cellular function. The Src homology (SH)2 domain is an important conductor of intracellular signaling that binds to phosphorylated tyrosines on acceptor proteins, producing molecular complexes responsible for signal relay. Cortactin is a cytoskeletal protein and tyrosine kinase substrate that regulates actin-based motility through interactions with SH2-domain-containing proteins. The Src kinase SH2 domain mediates cortactin binding and tyrosine phosphorylation, but how Src interacts with cortactin is unknown. Here we demonstrate that Src binds cortactin through cystine bonding between Src C185 in the SH2 domain within the phosphotyrosine binding pocket and cortactin C112/246 in the cortactin repeats domain, independent of tyrosine phosphorylation. Interaction studies show that the presence of reducing agents ablates Src-cortactin binding, eliminates cortactin phosphorylation by Src, and prevents Src SH2 domain binding to cortactin. Tandem MS/MS sequencing demonstrates cystine bond formation between Src C185 and cortactin C112/246. Mutational studies indicate that an intact cystine binding interface is required for Src-mediated cortactin phosphorylation, cell migration, and pre-invadopodia formation. Our results identify a novel phosphotyrosine-independent binding mode between the Src SH2 domain and cortactin. Besides Src, one quarter of all SH2 domains contain cysteines at or near the analogous Src C185 position. This provides a potential alternative mechanism to tyrosine phosphorylation for cysteine-containing SH2 domains to bind cognate ligands that may be widespread in propagating signals regulating diverse cellular functions.
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Affiliation(s)
- Jason V Evans
- Department of Neurobiology and Anatomy, Program in Cancer Cell Biology, Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
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88
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Heuckmann JM, Rauh D, Thomas RK. Epidermal Growth Factor Receptor (EGFR) Signaling and Covalent EGFR Inhibition in Lung Cancer. J Clin Oncol 2012; 30:3417-20. [DOI: 10.1200/jco.2012.43.1825] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Daniel Rauh
- Technical University Dortmund, Dortmund, Germany
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89
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Pershad K, Wypisniak K, Kay BK. Directed evolution of the forkhead-associated domain to generate anti-phosphospecific reagents by phage display. J Mol Biol 2012; 424:88-103. [PMID: 22985966 DOI: 10.1016/j.jmb.2012.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/10/2012] [Accepted: 09/05/2012] [Indexed: 10/27/2022]
Abstract
While affinity reagents are valuable tools for monitoring protein phosphorylation and studying signaling events in cells, generating them through immunization of animals with phosphopeptides is expensive, laborious, and time-consuming. An attractive alternative is to use protein evolution techniques and isolate new anti-phosphopeptide binding specificities from a library of variants of a phosphopeptide-binding domain. To explore this strategy, we attempted to display on the surface of bacteriophage M13 the N-terminal Forkhead-associated (FHA1) domain of yeast Rad53p, which is a naturally occurring phosphothreonine (pT)-binding domain, and found it to be nonfunctional due to misfolding in the bacterial periplasm. To overcome this limitation, we constructed a library of FHA1 variants by mutagenic PCR and isolated functional variants after three rounds of affinity selection with its pT peptide ligand. A hydrophobic residue at position 34 in the β1 strand was discovered to be essential for phage display of a functional FHA1 domain. Additionally, by heating the phage library to 50°C prior to affinity selection with its cognate pT peptide, we identified a variant (G2) that was ~8°C more thermally stable than the wild-type domain. Using G2 as a scaffold, we constructed phage-displayed libraries of FHA1 variants and affinity selected for variants that bound selectively to five pT peptides. These reagents are renewable and have high protein yields (~20-25mg/L), when expressed in Escherichia coli. Thus, we have changed the specificity of the FHA1 domain and demonstrated that engineering phosphopeptide-binding domains is an attractive avenue for generating new anti-phosphopeptide binding specificities in vitro by phage display.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, Laboratory for Molecular Biology (M/C 567), University of Illinois at Chicago, Molecular Biology Research Building, Chicago, IL 60607, USA.
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90
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Hause RJ, Leung KK, Barkinge JL, Ciaccio MF, Chuu CP, Jones RB. Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors. PLoS One 2012; 7:e44471. [PMID: 22973453 PMCID: PMC3433420 DOI: 10.1371/journal.pone.0044471] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/08/2012] [Indexed: 11/30/2022] Open
Abstract
First-generation interaction maps of Src homology 2 (SH2) domains with receptor tyrosine kinase (RTK) phosphosites have previously been generated using protein microarray (PM) technologies. Here, we developed a large-scale fluorescence polarization (FP) methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB) domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry procedures. This dataset represents a rich source of testable hypotheses regarding the biological mechanisms of ErbB receptors.
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Affiliation(s)
- Ronald J. Hause
- The Committee on Genetics, Genomics, and Systems Biology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, United States of America
| | - Kin K. Leung
- The Committee on Cancer Biology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, United States of America
| | - John L. Barkinge
- The Committee on Genetics, Genomics, and Systems Biology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, United States of America
| | - Mark F. Ciaccio
- The Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, United States of America
| | - Chih-pin Chuu
- Institute of Cellular and System Medicine, and Translational Center for Glandular Malignancies, National Health Research Institutes, Miaoli, Taiwan
| | - Richard B. Jones
- The Committee on Genetics, Genomics, and Systems Biology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, United States of America
- The Committee on Cancer Biology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, United States of America
- The Committee on Cellular and Molecular Physiology, The Ben May Department for Cancer Research and the Institute for Genomics and Systems Biology, The Gwen and Jules Knapp Center for Biomedical Discovery, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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91
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Kopp K, Buntru A, Pils S, Zimmermann T, Frank R, Zumbusch A, Hauck CR. Grb14 is a negative regulator of CEACAM3-mediated phagocytosis of pathogenic bacteria. J Biol Chem 2012; 287:39158-70. [PMID: 22948154 DOI: 10.1074/jbc.m112.395228] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Carcinoembryonic antigen-related cell adhesion molecule 3 (CEACAM3) is a phagocytic receptor on human granulocytes, which mediates the opsonin-independent recognition and internalization of a restricted set of Gram-negative bacteria such as Neisseria gonorrhoeae. In an unbiased screen using a SH2 domain microarray we identified the SH2 domain of growth factor receptor-bound protein 14 (Grb14) as a novel binding partner of CEACAM3. Biochemical assays and microscopic studies demonstrated that the Grb14 SH2 domain promoted the rapid recruitment of this adaptor protein to the immunoreceptor-based activation motif (ITAM)-like sequence within the cytoplasmic domain of CEACAM3. Furthermore, FRET-FLIM analyses confirmed the direct association of Grb14 and CEACAM3 in intact cells at the sites of bacteria-host cell contact. Knockdown of endogenous Grb14 by RNA interference as well as Grb14 overexpression indicate an inhibitory role for this adapter protein in CEACAM3-mediated phagocytosis. Therefore, Grb14 is the first negative regulator of CEACAM3-initiated bacterial phagocytosis and might help to focus granulocyte responses to the subcellular sites of pathogen-host cell contact.
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Affiliation(s)
- Kathrin Kopp
- Lehrstuhl Zellbiologie, Universität Konstanz, 78457 Konstanz, Germany
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92
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Fast rebinding increases dwell time of Src homology 2 (SH2)-containing proteins near the plasma membrane. Proc Natl Acad Sci U S A 2012; 109:14024-9. [PMID: 22886086 DOI: 10.1073/pnas.1203397109] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) control a host of biological functions by phosphorylating tyrosine residues of intracellular proteins upon extracellular ligand binding. The phosphotyrosines (p-Tyr) then recruit a subset of ∼100 Src homology 2 (SH2) domain-containing proteins to the cell membrane. The in vivo kinetics of this process are not well understood. Here we use total internal reflection (TIR) microscopy and single-molecule imaging to monitor interactions between SH2 modules and p-Tyr sites near the cell membrane. We found that the dwell time of SH2 modules within the TIR illumination field is significantly longer than predictions based on chemical dissociation rate constants, suggesting that SH2 modules quickly rebind to nearby p-Tyr sites after dissociation. We also found that, consistent with the rebinding model, the effective diffusion constant is negatively correlated with the respective dwell time for different SH2 domains and the dwell time is positively correlated with the local density of RTK phosphorylation. These results suggest a mechanism whereby signal output can be regulated through the spatial organization of multiple binding sites, which will prompt reevaluation of many aspects of RTK signaling, such as signaling specificity, mechanisms of spatial control, and noise suppression.
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93
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Abstract
Prolactin and the prolactin receptors are members of a family of hormone/receptor pairs which include GH, erythropoietin, and other ligand/receptor pairs. The mechanisms of these ligand/receptor pairs have broad similarities, including general structures, ligand/receptor stoichiometries, and activation of several common signaling pathways. But significant variations in the structural and mechanistic details are present among these hormones and their type 1 receptors. The prolactin receptor is particularly interesting because it can be activated by three sequence-diverse human hormones: prolactin, GH, and placental lactogen. This system offers a unique opportunity to compare the detailed molecular mechanisms of these related hormone/receptor pairs. This review critically evaluates selected literature that informs these mechanisms, compares the mechanisms of the three lactogenic hormones, compares the mechanism with those of other class 1 ligand/receptor pairs, and identifies information that will be required to resolve mechanistic ambiguities. The literature describes distinct mechanistic differences between the three lactogenic hormones and their interaction with the prolactin receptor and describes more significant differences between the mechanisms by which other related ligands interact with and activate their receptors.
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Affiliation(s)
- Charles L Brooks
- Departments of Veterinary Biosciences and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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94
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Mayer BJ. Perspective: Dynamics of receptor tyrosine kinase signaling complexes. FEBS Lett 2012; 586:2575-9. [PMID: 22584051 DOI: 10.1016/j.febslet.2012.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 04/30/2012] [Accepted: 05/02/2012] [Indexed: 11/17/2022]
Abstract
Textbook descriptions of signal transduction complexes provide a static snapshot view of highly dynamic events. Despite enormous strides in identifying the key components of signaling complexes and the underlying mechanisms of signal transduction, our understanding of the dynamic behavior of these complexes has lagged behind. Using the example of receptor tyrosine kinases, this perspective takes a fresh look at the dynamics of the system and their potential impact on signal processing.
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Affiliation(s)
- Bruce J Mayer
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA.
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95
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Mouchemore KA, Pixley FJ. CSF-1 signaling in macrophages: pleiotrophy through phosphotyrosine-based signaling pathways. Crit Rev Clin Lab Sci 2012; 49:49-61. [DOI: 10.3109/10408363.2012.666845] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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96
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Mueller D, Tegtmeyer N, Brandt S, Yamaoka Y, De Poire E, Sgouras D, Wessler S, Torres J, Smolka A, Backert S. c-Src and c-Abl kinases control hierarchic phosphorylation and function of the CagA effector protein in Western and East Asian Helicobacter pylori strains. J Clin Invest 2012; 122:1553-66. [PMID: 22378042 PMCID: PMC3314471 DOI: 10.1172/jci61143] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 01/11/2012] [Indexed: 12/24/2022] Open
Abstract
Many bacterial pathogens inject into host cells effector proteins that are substrates for host tyrosine kinases such as Src and Abl family kinases. Phosphorylated effectors eventually subvert host cell signaling, aiding disease development. In the case of the gastric pathogen Helicobacter pylori, which is a major risk factor for the development of gastric cancer, the only known effector protein injected into host cells is the oncoprotein CagA. Here, we followed the hierarchic tyrosine phosphorylation of H. pylori CagA as a model system to study early effector phosphorylation processes. Translocated CagA is phosphorylated on Glu-Pro-Ile-Tyr-Ala (EPIYA) motifs EPIYA-A, EPIYA-B, and EPIYA-C in Western strains of H. pylori and EPIYA-A, EPIYA-B, and EPIYA-D in East Asian strains. We found that c-Src only phosphorylated EPIYA-C and EPIYA-D, whereas c-Abl phosphorylated EPIYA-A, EPIYA-B, EPIYA-C, and EPIYA-D. Further analysis revealed that CagA molecules were phosphorylated on 1 or 2 EPIYA motifs, but never simultaneously on 3 motifs. Furthermore, none of the phosphorylated EPIYA motifs alone was sufficient for inducing AGS cell scattering and elongation. The preferred combination of phosphorylated EPIYA motifs in Western strains was EPIYA-A and EPIYA-C, either across 2 CagA molecules or simultaneously on 1. Our study thus identifies a tightly regulated hierarchic phosphorylation model for CagA starting at EPIYA-C/D, followed by phosphorylation of EPIYA-A or EPIYA-B. These results provide insight for clinical H. pylori typing and clarify the role of phosphorylated bacterial effector proteins in pathogenesis.
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Affiliation(s)
- Doreen Mueller
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Nicole Tegtmeyer
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Sabine Brandt
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Yoshio Yamaoka
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Eimear De Poire
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Dionyssios Sgouras
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Silja Wessler
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Javier Torres
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Adam Smolka
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Steffen Backert
- University of Magdeburg, Department of Medical Microbiology, Magdeburg, Germany.
University College Dublin, School of Biomolecular and Biomedical Sciences, Dublin, Ireland.
Michael E. DeBakey Veterans Affairs Medical Center and Baylor College of Medicine, Department Medicine-Gastroenterology, Houston, Texas, USA.
Oita University Faculty of Medicine, Department Environmental and Preventive Medicine, Yufu, Japan.
Hellenic Pasteur Institute, Laboratory of Medical Microbiology, Athens, Greece.
Division of Microbiology, University Salzburg, Salzburg, Austria.
Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatria, IMSS, Mexico.
Department of Medicine/Gastroenterology, Medical University of South Carolina, Charleston, South Carolina, USA
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97
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Huculeci R, Buts L, Lenaerts T, van Nuland NAJ, Garcia-Pino A. Purification, crystallization and preliminary X-ray diffraction analysis of the Fyn SH2 domain and its complex with a phosphotyrosine peptide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:359-64. [PMID: 22442244 PMCID: PMC3310552 DOI: 10.1107/s1744309112004186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 01/31/2012] [Indexed: 11/10/2022]
Abstract
SH2 domains are widespread protein-binding modules that recognize phosphotyrosines and play central roles in intracellular signalling pathways. The SH2 domain of the human protein tyrosine kinase Fyn has been expressed, purified and crystallized in the unbound state and in complex with a high-affinity phosphotyrosine peptide. X-ray data were collected to a resolution of 2.00 Å for the unbound form and 1.40 Å for the protein in complex with the phosphotyrosine peptide.
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Affiliation(s)
- Radu Huculeci
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Lieven Buts
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Tom Lenaerts
- MLG, Département d’Informatique, Université Libre de Bruxelles, Boulevard du Triomphe CP212, B-1050 Brussels, Belgium
- AI-lab, Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Nico A. J. van Nuland
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Abel Garcia-Pino
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
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98
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Baregamian N, Song J, Chung DH. Effects of oxidative stress on intestinal type I insulin-like growth factor receptor expression. Eur J Pediatr Surg 2012; 22:97-104. [PMID: 22434232 PMCID: PMC4313734 DOI: 10.1055/s-0032-1306261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Oxidative stress activates multiple signaling transduction pathways, including the phosphatidylinositol 3-kinase (PI3-K), in an injured intestine as occurs in necrotizing enterocolitis (NEC). We have previously shown that hydrogen peroxide (H2O2)-induced PI3-K activation is significantly enhanced with exogenous insulin-like growth factor (IGF)-1 in intestinal epithelial cells. However, the effects of oxidative stress on IGF receptor type I (IGF-IR) activation and expression in the neonatal intestine during NEC are unknown. MATERIAL AND METHODS Intestinal sections from neonates undergoing bowel resections (control = 3, NEC = 20) were analyzed for IGF-IR expression. NEC was induced in newborn mouse pups using hypoxia and hyperosmolar feeds, and distal small bowel segments were analyzed for IGF-IR expression (control = 3, NEC = 7). H2O2 was used to induce oxidative stress in rat (RIE-1) and fetal human (FHs74 Int) intestinal epithelial cells. Phosphorylation of IGF-IR, Akt, a downstream effector of PI3-K, and IGF-IR levels were determined by Western blotting. Flow cytometry, immunofluorescence, immunohistochemistry, IGF-IR tyrosine phosphorylation array, cell death enzyme-linked immunosorbent assay, and Western blotting were used to determine the IGF-IR expression. RESULTS An increased IGF-IR expression was noted in intestinal sections from NEC as well as murine model of NEC. H2O2 treatment rapidly activated IGF-IR and increased the expression in RIE-1 and FHs74 Int cells. Inhibition of IGF-IR resulted in significant RIE-1 cell apoptosis during oxidative stress. IGF-IR tyrosine phosphorylation array showed the recruitment of several key SH2 domain-containing proteins and oncogenes to the IGF-IR tyrosine kinase domain in H2O2-treated RIE-1 cells. CONCLUSION IGF-IR-mediated activation of intracellular signaling may play a critical role during oxidative stress-induced apoptosis in NEC.
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Affiliation(s)
- Naira Baregamian
- Department of Surgery, University of Texas Medical Branch, Galveston, Texas
| | - Jun Song
- Markey Cancer Center, University of Kentucky, Lexington, KY
| | - Dai H. Chung
- Departments of Pediatric Surgery and Cancer Biology Vanderbilt University Medical Center, Nashville, TN
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99
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Zou L, Cao S, Kang N, Huebert RC, Shah VH. Fibronectin induces endothelial cell migration through β1 integrin and Src-dependent phosphorylation of fibroblast growth factor receptor-1 at tyrosines 653/654 and 766. J Biol Chem 2012; 287:7190-202. [PMID: 22247553 DOI: 10.1074/jbc.m111.304972] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The extracellular matrix microenvironment regulates cell phenotype and function. One mechanism by which this is achieved is the transactivation of receptor tyrosine kinases by specific matrix molecules. Here, we demonstrate that the provisional matrix protein, fibronectin (FN), activates fibroblast growth factor (FGF) receptor-1 (FGFR1) independent of FGF ligand in liver endothelial cells. FN activation of FGFR1 requires β1 integrin, as evidenced by neutralizing antibody and siRNA-based studies. Complementary genetic and pharmacologic approaches identify that the non-receptor tyrosine kinase Src is required for FN transactivation of FGFR1. Whereas FGF ligand-induced phosphorylation of FGFR1 preferentially activates ERK, FN-induced phosphorylation of FGFR1 preferentially activates AKT, indicating differential downstream signaling of FGFR1 in response to alternate stimuli. Mutation analysis of known tyrosine residues of FGFR1 reveals that tyrosine 653/654 and 766 residues are required for FN-FGFR1 activation of AKT and chemotaxis. Thus, our study mechanistically dissects a new signaling pathway by which FN achieves endothelial cell chemotaxis, demonstrates how differential phosphorylation profiles of FGFR1 can achieve alternate downstream signals, and, more broadly, highlights the diversity of mechanisms by which the extracellular matrix microenvironment regulates cell behavior through transactivation of receptor tyrosine kinases.
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Affiliation(s)
- Li Zou
- Gastroenterology Research Unit and Cancer Cell Biology Program, Mayo Clinic, Rochester, Minnesota 55905, USA
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100
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Analysis of protein-protein interaction using proteinchip array-based SELDI-TOF mass spectrometry. Methods Mol Biol 2012; 818:217-26. [PMID: 22083826 PMCID: PMC3369541 DOI: 10.1007/978-1-61779-418-6_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein-protein interactions are key elements in the assembly of cellular regulatory and signaling protein complexes that integrate and transmit signals and information in controlling and regulating various cellular processes and functions. Many conventional methods of studying protein-protein interaction, such as the immuno-precipitation and immuno-blotting assay and the affinity-column pull-down and chromatographic analysis, are very time-consuming and labor intensive and lack accuracy and sensitivity. We have developed a simple, rapid, and sensitive assay using a ProteinChip array and SELDI-TOF mass spectrometry to analyze protein-protein interactions and map the crucial elements that are directly involved in these interactions. First, a purified "bait" protein or a synthetic peptide of interest is immobilized onto the preactivated surface of a PS10 or PS20 ProteinChip and the unoccupied surfaces on the chip are protected by application of a layer ethanolamine to prevent them from binding to other non-interactive proteins. Then, the target-containing cellular protein lysate or synthetic peptide containing the predicted amino acid sequence of protein-interaction motif is applied to the protected array with immobilized bait protein/peptide. The nonspecific proteins/peptides are washed off under various stringent conditions and only the proteins specifically interacting with the bait protein/peptide remain on the chip. Last, the captured interacting protein/peptide complexes are then analyzed by SELDI-TOF mass spectrometry and their identities are confirmed by their predicted distinctive masses. This method can be used to unambiguously detect the specific protein-protein interaction of known proteins/peptides, to easily identify potential cellular targets of proteins of interest, and to accurately analyze and map the structural elements of a given protein and its target proteins using synthetic peptides with the predicted potential protein interaction motifs.
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