Professional Education

  • PhD, Pohang University of Science and Technology, Signaling Proteome (2006)

Stanford Advisors


All Publications

  • Ultrasensitivity part II: multisite phosphorylation, stoichiometric inhibitors, and positive feedback TRENDS IN BIOCHEMICAL SCIENCES Ferrell, J. E., Ha, S. H. 2014; 39 (11): 556-569
  • Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity TRENDS IN BIOCHEMICAL SCIENCES Ferrell, J. E., Ha, S. H. 2014; 39 (10): 496-503
  • Ultrasensitivity part III: cascades, bistable switches, and oscillators. Trends in biochemical sciences Ferrell, J. E., Ha, S. H. 2014; 39 (12): 612-8


    Switch-like, ultrasensitive responses - responses that resemble those of cooperative enzymes but are not necessarily generated by cooperativity - are widespread in signal transduction. In the previous installments in this series, we reviewed several mechanisms for generating ultrasensitivity: zero-order ultrasensitivity; multistep ultrasensitivity; inhibitor ultrasensitivity; and positive feedback (or double negative feedback) loops. In this review, we focus on how ultrasensitive components can be important for the functioning of more complex signaling circuits. Ultrasensitivity can allow the effective transmission of signals down a signaling cascade, can contribute to the generation of bistability by positive feedback, and can promote the production of biochemical oscillations in negative feedback loops. This makes ultrasensitivity a key building block in systems biology and synthetic biology.

    View details for DOI 10.1016/j.tibs.2014.10.002

    View details for PubMedID 25456048

  • Leucyl-tRNA Synthetase Is an Intracellular Leucine Sensor for the mTORC1-Signaling Pathway CELL Han, J. M., Jeong, S. J., Park, M. C., Kim, G., Kwon, N. H., Kim, H. K., Ha, S. H., Ryu, S. H., Kim, S. 2012; 149 (2): 410-424


    Amino acids are required for activation of the mammalian target of rapamycin (mTOR) kinase, which regulates protein translation, cell size, and autophagy. However, the amino acid sensor that directly couples intracellular amino acid-mediated signaling to mTORC1 is unknown. Here we show that leucyl-tRNA synthetase (LRS) plays a critical role in amino acid-induced mTORC1 activation by sensing intracellular leucine concentration and initiating molecular events leading to mTORC1 activation. Mutation of LRS amino acid residues important for leucine binding renders the mTORC1 pathway insensitive to intracellular levels of amino acids. We show that LRS directly binds to Rag GTPase, the mediator of amino acid signaling to mTORC1, in an amino acid-dependent manner and functions as a GTPase-activating protein (GAP) for Rag GTPase to activate mTORC1. This work demonstrates that LRS is a key mediator for amino acid signaling to mTORC1.

    View details for DOI 10.1016/j.cell.2012.02.044

    View details for Web of Science ID 000302805600019

    View details for PubMedID 22424946

  • Supramolecular fishing for plasma membrane proteins using an ultrastable synthetic host-guest binding pair NATURE CHEMISTRY Lee, D., Park, K. M., Banerjee, M., Ha, S. H., Lee, T., Suh, K., Paul, S., Jung, H., Kim, J., Selvapalam, N., Ryu, S. H., Kim, K. 2011; 3 (2): 154-159


    Membrane proteomics, the large-scale global analysis of membrane proteins, is often constrained by the efficiency of separating and extracting membrane proteins. Recent approaches involve conjugating membrane proteins with the small molecule biotin and using the receptor streptavidin to extract the labelled proteins. Despite the many advantages of this method, several shortcomings remain, including potential contamination by endogenously biotinylated molecules and interference by streptavidin during analytical stages. Here, we report a supramolecular fishing method for membrane proteins using the synthetic receptor-ligand pair cucurbit[7]uril-1-trimethylammoniomethylferrocene (CB[7]-AFc). CB[7]-conjugated beads selectively capture AFc-labelled proteins from heterogeneous protein mixtures, and AFc-labelling of cells results in the efficient capture of membrane proteins by these beads. The captured proteins can be recovered easily at room temperature by treatment with a strong competitor such as 1,1'-bis(trimethylammoniomethyl)ferrocene. This synthetic but biocompatible host-guest system may be a useful alternative to streptavidin-biotin for membrane proteomics as well as other biological and biotechnological applications.

    View details for DOI 10.1038/NCHEM.928

    View details for Web of Science ID 000286505700013

    View details for PubMedID 21258389

  • Cyclic AMP Controls mTOR through Regulation of the Dynamic Interaction between Rheb and Phosphodiesterase 4D MOLECULAR AND CELLULAR BIOLOGY Kim, H. W., Ha, S. H., Lee, M. N., Huston, E., Kim, D., Jang, S. K., Suh, P., Houslay, M. D., Ryu, S. H. 2010; 30 (22): 5406-5420


    The mammalian target of rapamycin complex 1 (mTORC1) is a molecular hub that regulates protein synthesis in response to a number of extracellular stimuli. Cyclic AMP (cAMP) is considered to be an important second messenger that controls mTOR; however, the signaling components of this pathway have not yet been elucidated. Here, we identify cAMP phosphodiesterase 4D (PDE4D) as a binding partner of Rheb that acts as a cAMP-specific negative regulator of mTORC1. Under basal conditions, PDE4D binds Rheb in a noncatalytic manner that does not require its cAMP-hydrolyzing activity and thereby inhibits the ability of Rheb to activate mTORC1. However, elevated cAMP levels disrupt the interaction of PDE4D with Rheb and increase the interaction between Rheb and mTOR. This enhanced Rheb-mTOR interaction induces the activation of mTORC1 and cap-dependent translation, a cellular function of mTORC1. Taken together, our results suggest a novel regulatory mechanism for mTORC1 in which the cAMP-determined dynamic interaction between Rheb and PDE4D provides a key, unique regulatory event. We also propose a new role for PDE4 as a molecular transducer for cAMP signaling.

    View details for DOI 10.1128/MCB.00217-10

    View details for Web of Science ID 000283656700013

    View details for PubMedID 20837708

  • Protein Kinase C delta-Mediated Phosphorylation of Phospholipase D Controls Integrin-Mediated Cell Spreading MOLECULAR AND CELLULAR BIOLOGY Chae, Y. C., Kim, K. L., Ha, S. H., Kim, J., Suh, P., Ryu, S. H. 2010; 30 (21): 5086-5098


    Integrin signaling plays critical roles in cell adhesion, spreading, and migration, and it is generally accepted that to regulate these integrin functions accurately, localized actin remodeling is required. However, the molecular mechanisms that control the targeting of actin regulation molecules to the proper sites are unknown. We previously demonstrated that integrin-mediated cell spreading and migration on fibronectin are dependent on the localized activation of phospholipase D (PLD). However, the mechanism underlying PLD activation by integrin is largely unknown. Here we demonstrate that protein kinase C? (PKC?) is required for integrin-mediated PLD signaling. After integrin stimulation, PKC? is activated and translocated to the edges of lamellipodia, where it colocalizes with PLD2. The abrogation of PKC? activity inhibited integrin-induced PLD activation and cell spreading. Finally, we show that Thr566 of PLD2 is directly phosphorylated by PKC? and that PLD2 mutation in this region prevents PLD2 activation, PLD2 translocation to the edge of lamellipodia, Rac translocation, and cell spreading after integrin activation. Together, these results suggest that PKC? is a primary regulator of integrin-mediated PLD activation via the direct phosphorylation of PLD, which is essential for directing integrin-induced cell spreading.

    View details for DOI 10.1128/MCB.00443-10

    View details for Web of Science ID 000282748600009

    View details for PubMedID 20733000

  • Comparative analysis of the secretory proteome of human adipose stromal vascular fraction cells during adipogenesis PROTEOMICS Kim, J., Choi, Y. S., Lim, S., Yea, K., Yoon, J. H., Jun, D., Ha, S. H., Kim, J., Kim, J. H., Suh, P., Ryu, S. H., Lee, T. G. 2010; 10 (3): 394-405


    Adipogenesis is a complex process that is accompanied by a number of molecular events. In this study, a proteomic approach was adopted to identify secretory factors associated with adipogenesis. A label-free shotgun proteomic strategy was implemented to analyze proteins secreted by human adipose stromal vascular fraction cells and differentiated adipocytes. A total of 474 proteins were finally identified and classified according to quantitative changes and statistical significances. Briefly, 177 proteins were significantly upregulated during adipogenesis (Class I), whereas 60 proteins were significantly downregulated (Class II). Changes in the expressions of several proteins were confirmed by quantitative RT-PCR and immunoblotting. One obvious finding based on proteomic data was that the amounts of several extracellular modulators of Wnt and transforming growth factor-beta (TGF-beta) signaling changed during adipogenesis. The expressions of secreted frizzled-related proteins, dickkopf-related proteins, and latent TGF-beta-binding proteins were found to be altered during adipogenesis, which suggests that they participate in the fine regulation of Wnt and TGF-beta signaling. This study provides useful tools and important clues regarding the roles of secretory factors during adipogenic differentiation, and provides information related to obesity and obesity-related metabolic diseases.

    View details for DOI 10.1002/pmic.200900218

    View details for Web of Science ID 000274707400004

    View details for PubMedID 19953544

  • Collapsin response mediator protein-2 regulates neurite formation by modulating tubulin GTPase activity CELLULAR SIGNALLING Chae, Y. C., Lee, S., Heo, K., Ha, S. H., Jung, Y., Kim, J. H., Ihara, Y., Suh, P., Ryu, S. H. 2009; 21 (12): 1818-1826


    Collapsin response mediator protein-2 (CRMP-2) plays a key role in axonal development by regulating microtubule dynamics. However, the molecular mechanisms underlying this function have not been clearly elucidated. In this study, we demonstrated that hCRMP-2, specifically amino acid residues 480-509, is essential for stimulating tubulin GTPase activity. We also found that the GTPase-activating protein (GAP) activity of hCRMP-2 was important for microtubule assembly and neurite formation in differentiated PC12 pheochromocytoma cell lines. Mutant hCRMP-2, lacking arginine residues responsible for GAP activity, inhibited microtubule assembly and neurite formation. Interestingly, we found that the N-terminal region (amino acids150-299) of hCRMP-2 had an inhibitory role on GAP activity via a direct interaction with the C-terminal region (amino acids 480-509). Our results suggest that CRMP-2 as a tubulin direct binder may be a GAP of tubulin in neurite formation and that its GAP activity may be regulated by an intramolecular interaction with an N-terminal inhibitory region.

    View details for DOI 10.1016/j.cellsig.2009.07.017

    View details for Web of Science ID 000271269900011

    View details for PubMedID 19666111

  • Phosphorylation of Phospholipase C-delta(1) Regulates its Enzymatic Activity JOURNAL OF CELLULAR BIOCHEMISTRY Fujii, M., Yi, K. S., Kim, M. J., Ha, S. H., Ryu, S. H., Suh, P., Yagisawa, H. 2009; 108 (3): 638-650


    Phosphorylation of phospholipase C-delta(1) (PLC-delta(1)) in vitro and in vivo was investigated. Of the serine/threonine kinases tested, protein kinase C (PKC) phosphorylated the serine residue(s) of bacterially expressed PLC-delta(1) most potently. It was also demonstrated that PLC-delta(1) directly bound PKC-alpha via its pleckstrin homology (PH) domain. Using deletion mutants of PLC-delta(1) and synthetic peptides, Ser35 in the PH domain was defined as the PKC mediated in vitro phosphorylation site of PLC-delta(1). In vitro phosphorylation of PLC-delta(1) by PKC stimulated [(3)H]PtdIns(4,5)P(2) hydrolyzing activity and [(3)H]Ins(1,4,5)P(3)-binding of the PLC-delta(1). On the other hand, endogenous PLC-delta(1) was constitutively phosphorylated and phosphoamino acid analysis revealed that major phosphorylation sites were threonine residues in quiescent cells. The phosphorylation level and the species of phosphoamino acid were not changed by various stimuli such as PMA, EGF, NGF, and forskolin. Using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, we determined that Thr209 of PLC-delta(1) is one of the constitutively phosphorylated sites in quiescent cells. The PLC activity was potentiated when constitutively phosphorylated PLC-delta(1) was dephosphorylated by endogenous phosphatase(s) in vitro. Additionally, coexpression with PKC-alpha reduced serine phosphorylation of PLC-delta(1) detected by an anti-phosphoserine antibody and PLC-delta(1)-dependent basal production of inositol phosphates in NIH-3T3 cells, suggesting PKC-alpha activates phosphatase or inactivates another kinase involved in PLC-delta(1) serine phosphorylation to modulate the PLC-delta(1) activity in vivo. Taken together, these results suggest that PLC-delta(1) has multiple phosphorylation sites and phosphorylation status of PLC-delta(1) regulates its activity positively or negatively depends on the phosphorylation sites.

    View details for DOI 10.1002/jcb.22297

    View details for Web of Science ID 000270567100011

    View details for PubMedID 19681039

  • Glycolytic Flux Signals to mTOR through Glyceraldehyde-3-Phosphate Dehydrogenase-Mediated Regulation of Rheb MOLECULAR AND CELLULAR BIOLOGY Lee, M. N., Ha, S. H., Kim, J., Koh, A., Lee, C. S., Kim, J. H., Jeon, H., Kim, D., Suh, P., Ryu, S. H. 2009; 29 (14): 3991-4001


    The mammalian target of rapamycin (mTOR) interacts with raptor to form the protein complex mTORC1 (mTOR complex 1), which plays a central role in the regulation of cell growth in response to environmental cues. Given that glucose is a primary fuel source and a biosynthetic precursor, how mTORC1 signaling is coordinated with glucose metabolism has been an important question. Here, we found that the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) binds Rheb and inhibits mTORC1 signaling. Under low-glucose conditions, GAPDH prevents Rheb from binding to mTOR and thereby inhibits mTORC1 signaling. High glycolytic flux suppresses the interaction between GAPDH and Rheb and thus allows Rheb to activate mTORC1. Silencing of GAPDH or blocking of the Rheb-GAPDH interaction desensitizes mTORC1 signaling to changes in the level of glucose. The GAPDH-dependent regulation of mTORC1 in response to glucose availability occurred even in TSC1-deficient cells and AMPK-silenced cells, supporting the idea that the GAPDH-Rheb pathway functions independently of the AMPK axis. Furthermore, we show that glyceraldehyde-3-phosphate, a glycolytic intermediate that binds GAPDH, destabilizes the Rheb-GAPDH interaction even under low-glucose conditions, explaining how high-glucose flux suppresses the interaction and activates mTORC1 signaling. Taken together, our results suggest that the glycolytic flux regulates mTOR's access to Rheb by regulating the Rheb-GAPDH interaction, thereby allowing mTORC1 to coordinate cell growth with glucose availability.

    View details for DOI 10.1128/MCB.00165-09

    View details for Web of Science ID 000267939300015

    View details for PubMedID 19451232

  • Phospholipase C-gamma 1 potentiates integrin-dependent cell spreading and migration through Pyk2/paxillin activation CELLULAR SIGNALLING Choi, J. H., Yang, Y., Lee, S. K., Kim, I., Ha, S. H., Kim, E., Bae, Y. S., Ryu, S. H., Suh, P. 2007; 19 (8): 1784-1796


    Phospholipase C-gamma1 (PLC-gamma1), which generates two second messengers, namely, inositol-1, 4, 5-trisphosphate and diacylglycerol, is implicated in growth factor-mediated chemotaxis. However, the exact role of PLC-gamma1 in integrin-mediated cell adhesion and migration remains poorly understood. In this study, we demonstrate that PLC-gamma1 is required for actin cytoskeletal organization and cell motility through the regulation of Pyk2 and paxillin activation. After fibronectin stimulation, PLC-gamma1 directly interacted with the cytoplasmic tail of integrin beta1. In PLC-gamma1-silenced cells, integrin-induced Pyk2 and paxillin phosphorylation were significantly reduced and PLC-gamma1 potentiated the integrin-induced Pyk2/paxillin activation in its enzymatic activity-dependent manner. In addition, specific knock-down of PLC-gamma1 resulted in a failure to form focal adhesions dependent on fibronectin stimulation, which appeared to be caused by the suppression of Pyk2 and paxillin phosphorylation. Interestingly, PLC-gamma1 potentiated the activations of Rac, thus integrin-induced lamellipodia formation was up-regulated. Consequently, the strength of cell-substratum interaction and cell motility were profoundly up-regulated by PLC-gamma1. Taken together, these results suggest that PLC-gamma1 is a key player in integrin-mediated cell spreading and motility achieved by the activation of Pyk2/paxillin/Rac signaling.

    View details for DOI 10.1016/j.cellsig.2007.04.002

    View details for Web of Science ID 000248175200017

    View details for PubMedID 17531443

  • PLD2 forms a functional complex with mTOR/raptor to transduce mitogenic signals CELLULAR SIGNALLING Ha, S. H., Kim, D., Kim, I., Kim, J. H., Lee, M. N., Lee, H. J., Kim, J. H., Jang, S. K., Suh, P., Ryu, S. H. 2006; 18 (12): 2283-2291


    Mammalian target-of-rapamycin (mTOR), which is a master controller of cell growth, senses a mitogenic signal in part through the lipid second messenger phosphatidic acid (PA), generated by phospholipase D (PLD). To understand further which isozymes of PLD are involved in this process, we compared the effect of PLD isozymes on mTOR activation. We found that PLD2 has an essential role in mitogen-induced mTOR activation as the siRNA-mediated knockdown of PLD2, not of PLD1, profoundly reduced the phosphorylations of S6K1 and 4EBP1, well-known mTOR effectors. Furthermore, exogenous PA-induced mTOR activation was abrogated by PLD2 knockdown, but not by PLD1 knockdown. This abrogation was found to be the result of complex formation between PLD2 and mTOR/raptor. PLD2 possesses a TOS-like motif (Phe-Glu-Val-Gln-Val, a.a. 265-269), through which it interacts with raptor independently of the other TOS motif-containing proteins, S6K1 and 4EBP1. PLD2-dependent mTOR activation appears to require PLD2 binding to mTOR/raptor with lipase activity, since lipase-inactive PLD2 cannot trigger mTOR activation despite its ability to interact with mTOR/raptor. Abrogation of mitogen-dependent mTOR activation by PLD2 knockdown was rescued only by wild type PLD2, but not by raptor binding-deficient and lipase-inactive PLD2. Our results demonstrate the importance of localized PA generation for the mitogen-induced activation of mTOR, which is achieved by a specific interaction between PLD2 and mTOR/raptor.

    View details for DOI 10.1016/j.cellsig.2006.05.021

    View details for Web of Science ID 000242266400022

    View details for PubMedID 16837165

  • RGS2 promotes formation of neurites by stimulating microtubule polymerization CELLULAR SIGNALLING Heo, K., Ha, S. H., Chae, Y. C., Lee, S., Oh, Y., Kim, Y., Kim, S., Kim, J. H., Mizoguchi, A., Itoh, T. J., Kwon, H. M., Ryu, S. H., Suh, P. 2006; 18 (12): 2182-2192


    Regulator of G-protein signaling (RGS) proteins interact with alpha subunits of heterotrimeric G-proteins via the RGS domain and attenuate their activity by accelerating GTPase activity. RGS2, a member of the RGS family, regulates synaptic development via hereto unknown mechanism. In this study, we found that RGS2 directly interacted with tubulin via a short region at the N-terminus: amino acids 41-60. RGS2 enhanced microtubule polymerization in vitro, and the tubulin binding region was necessary and sufficient for this activity. In Vero cells, polymerization of microtubule was stimulated when peptides containing the tubulin binding region were microinjected. Immunocytochemical analysis showed that endogenous RGS2 was localized at the termini of neurites in differentiated PC12 cells. Over-expression of RGS2 enhanced the nerve growth factor-induced neurite outgrowth in PC12 cells, while specific knock-down of endogenous RGS2 suppressed the neurite outgrowth. These findings demonstrate that RGS2 contributes to the neuronal cell differentiation via regulation of microtubule dynamics.

    View details for DOI 10.1016/j.cellsig.2006.05.006

    View details for Web of Science ID 000242266400012

    View details for PubMedID 16820281

  • Inositol 5 '-phosphatase, SHIP1 interacts with phospholipase C-gamma 1 and modulates EGF-induced PLC activity EXPERIMENTAL AND MOLECULAR MEDICINE Song, M., Kim, M. J., Ha, S., Park, J. B., Ryu, S. H., Suh, P. G. 2005; 37 (3): 161-168


    Phospholipase C-gamma1, containing two SH2 and one SH3 domains which participate in the interaction between signaling molecules, plays a significant role in the growth factor-induced signal transduction. However, the role of the SH domains in the growth factor-induced PLC-gamma1 regulation is unclear. By peptide-mass fingerprinting analysis, we have identified SHIP1 as the binding protein for the SH3 domain of PLC-gamma1. SHIP1 was co-immunoprecipitated with PLC-gamma1 and potentiated EGF-induced PLC-gamma1 activation. However, inositol 5'-phosphatase activity of SHIP1 was not required for the potentiation of EGF-induced PLC-gamma1 activation. Taken together, these results suggest that SHIP1 may function as an adaptor protein which can potentiate EGF-induced PLC-gamma1 activation without regards to its inositol 5'-phosphatase activity.

    View details for Web of Science ID 000230510800003

    View details for PubMedID 16000869

  • A cellular RNA-binding protein enhances internal ribosomal entry site-dependent translation through an interaction downstream of the Hepatitis C virus polyprotein initiation codon MOLECULAR AND CELLULAR BIOLOGY Kim, J. H., Paek, K. Y., Ha, S. H., Cho, S. C., Choi, K., Kim, C. S., Ryu, S. H., Jang, S. K. 2004; 24 (18): 7878-7890


    Translational initiation of hepatitis C virus (HCV) mRNA occurs by internal entry of ribosomes into an internal ribosomal entry site (IRES) at the 5' nontranslated region. A region encoding the N-terminal part of the HCV polyprotein has been shown to augment the translation of HCV mRNA. Here we show that a cellular protein, NS1-associated protein 1 (NSAP1), augments HCV mRNA translation through a specific interaction with an adenosine-rich protein-coding region within the HCV mRNA. The overexpression of NSAP1 specifically enhanced HCV IRES-dependent translation, and knockdown of NSAP1 by use of a small interfering RNA specifically inhibited the translation of HCV mRNA. An HCV replicon RNA capable of mimicking the HCV proliferation process in host cells was further used to confirm that NSAP1 enhances the translation of HCV mRNA. These results suggest the existence of a novel mechanism of translational enhancement that acts through the interaction of an RNA-binding protein with a protein coding sequence.

    View details for DOI 10.1128/MCB.24.18.7878.7890.2004

    View details for Web of Science ID 000223760600006

    View details for PubMedID 15340051

  • GABA(A) receptor phospho-dependent modulation is regulated by phospholipase C-related inactive protein type 1, a novel protein phosphatase 1 anchoring protein JOURNAL OF NEUROSCIENCE Terunuma, M., Jang, I. S., Ha, S. H., Kittler, J. T., Kanematsu, T., Jovanovic, J. N., Nakayama, K. I., Akaike, N., Ryu, S. H., Moss, S. J., Hirata, M. 2004; 24 (32): 7074-7084


    GABA(A) receptors are critical in controlling neuronal activity. Here, we examined the role for phospholipase C-related inactive protein type 1 (PRIP-1), which binds and inactivates protein phosphatase 1alpha (PP1alpha) in facilitating GABA(A) receptor phospho-dependent regulation using PRIP-1-/- mice. In wild-type animals, robust phosphorylation and functional modulation of GABA(A) receptors containing beta3 subunits by cAMP-dependent protein kinase was evident, which was diminished in PRIP-1-/- mice. PRIP-1-/- mice exhibited enhanced PP1alpha activity compared with controls. Furthermore, PRIP-1 was able to interact directly with GABA(A) receptor beta subunits, and moreover, these proteins were found to be PP1alpha substrates. Finally, phosphorylation of PRIP-1 on threonine 94 facilitated the dissociation of PP1alpha-PRIP-1 complexes, providing a local mechanism for the activation of PP1alpha. Together, these results suggest an essential role for PRIP-1 in controlling GABA(A) receptor activity via regulating subunit phosphorylation and thereby the efficacy of neuronal inhibition mediated by these receptors.

    View details for DOI 10.1523/JNEUROSCI.1323-04.2004

    View details for Web of Science ID 000223331100005

    View details for PubMedID 15306641

  • Analysis of insulin receptor signaling in HEK 293 cells FASEB JOURNAL Lee, H. J., Lee, B. D., Ha, S. H., Kim, K. I., Suh, P. G., Ryu, S. H. 2004; 18 (8): C251-C251
  • Identification of cellular proteins enhancing activities of internal ribosomal entry sites by competition with oligodeoxynucleotides NUCLEIC ACIDS RESEARCH Choi, K., Kim, J. H., Li, X. Y., Paek, K. Y., Ha, S. H., Ryu, S. H., Wimmer, E., Jang, S. K. 2004; 32 (4): 1308-1317


    The translation of numerous eukaryotic mRNAs is mediated by internal ribosomal entry sites (IRESs). IRES-dependent translation requires both canonical translation initiation factors and IRES-specific trans-acting factors (ITAFs). Here we report a strategy to identify and characterize ITAFs required for IRES-dependent translation. This process involves steps for identifying oligodeoxynucleotides affecting IRES-dependent translation, purifying proteins interacting with the inhibitory DNA, identifying the specific proteins with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry, and confirming the roles of these proteins in IRES-dependent translation by depletion and repletion of proteins from an in vitro translation system. Using this strategy, we show that poly(rC)-binding proteins 1 and 2 enhance translation through polioviral and rhinoviral IRES elements.

    View details for DOI 10.1093/nar/gkh300

    View details for Web of Science ID 000220179700015

    View details for PubMedID 14981151

  • Dynamic identification of phosphopeptides using immobilized metal ion affinity chromatography enrichment, subsequent partial beta-elimination/chemical tagging and matrix-assisted laser desorption/ionization mass spectrometric analysis RAPID COMMUNICATIONS IN MASS SPECTROMETRY Ahn, Y. H., Park, E. J., Cho, K., Kim, J. Y., Hal, S. H., Ryu, S. H., Yoo, J. S. 2004; 18 (20): 2495-2501


    The enrichment of phosphopeptides using immobilized metal ion affinity chromatography (IMAC) and subsequent mass spectrometric analysis is a powerful protocol for detecting phosphopeptides and analyzing their phosphorylation state. However, nonspecific binding peptides, such as acidic, nonphosphorylated peptides, often coelute and make analyses of mass spectra difficult. This study used a partial chemical tagging reaction of a phosphopeptide mixture, enriched by IMAC and contaminated with nonspecific binding peptides, following a modified beta-elimination/Michael addition method, and dynamic mass analysis of the resulting peptide pool. Mercaptoethanol was used as a chemical tag and nitrilotriacetic acid (NTA) immobilized on Sepharose beads was used for IMAC enrichment. The time-dependent dynamic mass analysis of the partially tagged reaction mixture detected intact phosphopeptides and their mercaptoethanol-tagged derivatives simultaneously by their mass difference (-20 Da for each phosphorylation site). The number of new peaks appearing with the mass shift gave the number of multiply phosphorylated sites in a phosphopeptide. Therefore, this partial chemical tagging/dynamic mass analysis method can be a powerful tool for rapid and efficient phosphopeptide identification and analysis of the phosphorylation state concurrently using only MS analysis data.

    View details for DOI 10.1002/rcm.1651

    View details for Web of Science ID 000224499400016

    View details for PubMedID 15384178

  • Hydrogen peroxide induces association between glyceraldehyde 3-phosphate dehydrogenase and phospholipase D2 to facilitate phospholipase D2 activation in PC12 cells JOURNAL OF NEUROCHEMISTRY Kim, J. H., Lee, S., Park, J. B., Lee, S. D., Kim, J. H., Ha, S. H., HASUMI, K., Endo, A., Suh, P. G., Ryu, S. H. 2003; 85 (5): 1228-1236


    Oxidative stress or signaling is widely implicated in apoptosis, ischemia and mitogenesis. Previously, our group reported that the hydrogen peroxide (H2O2)-dependent activation of phospholipase D2 (PLD2) in PC12 cells is involved in anti-apoptotic effect. However, the precise mechanism of PLD2 activation by H2O2 was not revealed. To find H2O2-dependent PLD2-regulating proteins, we immunoprecipitated PLD2 from PC12 cells and found that glyceraldehyde 3-phosphate dehydrogenase (GAPDH) coimmunoprecipitated with PLD2 upon H2O2 treatment. This interaction was found to be direct by in vitro reconstitution of purified GAPDH and PLD2. In vitro studies also indicated that PLD2-associated GAPDH was modified on its reactive cysteine residues. Koningic acid, an alkylator of GAPDH on catalytic cysteine residue, also increased interaction between the two proteins in vitro and enhanced PLD2 activity in PC12 cells. Blocking H2O2-dependent modification of GAPDH with 3-aminobenzamide resulted in the inhibition of the GAPDH/PLD2 interaction and attenuated H2O2-induced PLD2 activation in PC12 cells. From the results, we suggest that H2O2 modifies GAPDH on its catalytic cysteine residue not only to inactivate the dehydrogenase activity of GAPDH but also to endow GAPDH with the ability to bind PLD2 and the resulting association is involved in the regulation of PLD2 activity by H2O2.

    View details for DOI 10.1046/j.1471-4159.2003.01755.x

    View details for Web of Science ID 000182855400015

    View details for PubMedID 12753082

  • Cbl competitively inhibits epidermal growth factor-induced activation of phospholipase C-gamma 1 MOLECULES AND CELLS Choi, J. H., Bae, S. S., Park, J. B., Ha, S. H., Song, H., Kim, J. H., Cocco, L., Ryu, S. H., Suh, P. G. 2003; 15 (2): 245-255


    Phospholipase C-gamma1 (PLC-gamma1) plays pivotal roles in cellular growth and proliferation through its two Src homology (SH) 2 domains and its single SH3 domain, which interact with signaling molecules in response to various growth factors and hormones. However, the role of the SH domains in the growth factor-induced regulation of PLC-gamma1 is unclear. By peptide-mass fingerprinting analysis we have identified Cbl as a binding protein for the SH3 domain of PLC-gamma1 from rat pheochromatocyte PC12 cells. Association of Cbl with PLC-gamma1 was induced by epidermal growth factor (EGF) but not by nerve growth factor (NGF). Upon EGF stimulation, both Cbl and PLC-gamma1 were recruited to the activated EGF receptor through their SH2 domains. Mutation of the SH2 domains of either Cbl or PLC-gamma1 abrogated the EGF-induced interaction of PLC-gamma1 with Cbl, indicating that SH2-mediated translocation is essential for the association of PLC-gamma1 and Cbl. Overexpression of Cbl attenuated EGF-induced tyrosine phosphorylation and the subsequent activation of PLC-gamma1 by interfering competitively with the interaction between PLC-gamma1 and EGFR. Taken together, these results provide the first indications that Cbl may be a negative regulator of intracellular signaling following EGF-induced PLC-gamma1 activation.

    View details for Web of Science ID 000182588800016

    View details for PubMedID 12803489

  • Actin directly interacts with phospholipase D, inhibiting its activity JOURNAL OF BIOLOGICAL CHEMISTRY Lee, S., Park, J. B., Kim, J. H., Kim, Y., Kim, J. H., Shin, K. J., Lee, J. S., Ha, S. H., Suh, P. G., Ryu, S. H. 2001; 276 (30): 28252-28260


    Mammalian phospholipase D (PLD) plays a key role in several signal transduction pathways and is involved in many diverse functions. To elucidate the complex molecular regulation of PLD, we investigated PLD-binding proteins obtained from rat brain extract. Here we report that a 43-kDa protein in the rat brain, beta-actin, acts as a major PLD2 direct-binding protein as revealed by peptide mass fingerprinting in combination with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. We also determined that the region between amino acids 613 and 723 of PLD2 is required for the direct binding of beta-actin, using bacterially expressed glutathione S-transferase fusion proteins of PLD2 fragments. Intriguingly, purified beta-actin potently inhibited both phosphatidylinositol-4,5-bisphosphate- and oleate-dependent PLD2 activities in a concentration-dependent manner (IC50 = 5 nm). In a previous paper, we reported that alpha-actinin inhibited PLD2 activity in an interaction-dependent and an ADP-ribosylation factor 1 (ARF1)-reversible manner (Park, J. B., Kim, J. H., Kim, Y., Ha, S. H., Kim, J. H., Yoo, J.-S., Du, G., Frohman, M. A., Suh, P.-G., and Ryu, S. H. (2000) J. Biol. Chem. 275, 21295-21301). In vitro binding analyses showed that beta-actin could displace alpha-actinin binding to PLD2, demonstrating independent interaction between cytoskeletal proteins and PLD2. Furthermore, ARF1 could steer the PLD2 activity in a positive direction regardless of the inhibitory effect of beta-actin on PLD2. We also observed that beta-actin regulates PLD1 and PLD2 with similar binding and inhibitory potencies. Immunocytochemical and co-immunoprecipitation studies demonstrated the in vivo interaction between the two PLD isozymes and actin in cells. Taken together, these results suggest that the regulation of PLD by cytoskeletal proteins, beta-actin and alpha-actinin, and ARF1 may play an important role in cytoskeleton-related PLD functions.

    View details for Web of Science ID 000170093400069

    View details for PubMedID 11373276

  • Cardiac phospholipase D-2 localizes to sarcolemmal membranes and is inhibited by alpha-actinin in an ADP-ribosylation factor-reversible manner JOURNAL OF BIOLOGICAL CHEMISTRY Park, J. B., Kim, J. H., Kim, Y., Ha, S. H., Kim, J. H., Yoo, J. S., Du, G. W., Frohman, M. A., Suh, P. G., Ryu, S. H. 2000; 275 (28): 21295-21301


    Myocardial phospholipase D (PLD) has been implicated in the regulation of Ca(2+) mobilization and contractile performance in the heart. However, the molecular identity of this myocardial PLD and the mechanisms that regulate it are not well understood. Using subcellular fractionation and Western blot analysis, we found that PLD2 is the major myocardial PLD and that it localizes primarily to sarcolemmal membranes. A 100-kDa PLD2-interacting cardiac protein was detected using a protein overlay assay employing purified PLD2 and then identified as alpha-actinin using peptide-mass fingerprinting with matrix-assisted laser desorption/ionization mass spectroscopy. The direct association between PLD2 and alpha-actinin was confirmed using an in vitro binding assay and localized to PLD2's N-terminal 185 amino acids. Purified alpha-actinin potently inhibits PLD2 activity (IC(50) = 80 nm) in an interaction-dependent and ADP-ribosylation factor-reversible manner. Finally, alpha-actinin co-localizes with actin and with PLD2 in the detergent-insoluble fraction from sarcolemmal membranes. These results suggest that PLD2 is reciprocally regulated in sarcolemmal membranes by alpha-actinin and ARF1 and accordingly that a major role for PLD2 in cardiac function may involve reorganization of the actin cytoskeleton.

    View details for Web of Science ID 000088230600046

    View details for PubMedID 10801846

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