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Search Results: 1 - 10 of 8028 matches for " Seung-Wook Chi "
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Molecular Basis of Bcl-XL-p53 Interaction: Insights from Molecular Dynamics Simulations
Nagakumar Bharatham, Seung-Wook Chi, Ho Sup Yoon
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026014
Abstract: Bcl-XL, an antiapoptotic Bcl-2 family protein, plays a central role in the regulation of the apoptotic pathway. Heterodimerization of the antiapoptotic Bcl-2 family proteins with the proapoptotic family members such as Bad, Bak, Bim and Bid is a crucial step in the apoptotic regulation. In addition to these conventional binding partners, recent evidences reveal that the Bcl-2 family proteins also interact with noncanonical binding partners such as p53. Our previous NMR studies showed that Bcl-XL: BH3 peptide and Bcl-XL: SN15 peptide (a peptide derived from residues S15-N29 of p53) complex structures share similar modes of bindings. To further elucidate the molecular basis of the interactions, here we have employed molecular dynamics simulations coupled with MM/PBSA approach. Bcl-XL and other Bcl-2 family proteins have 4 hydrophobic pockets (p1–p4), which are occupied by four systematically spaced hydrophobic residues (h1–h4) of the proapoptotic Bad and Bak BH3 peptides. We observed that three conserved hydrophobic residues (F19, W23 and L26) of p53 (SN15) peptide anchor into three hydrophobic pockets (p2–p4) of Bcl-XL in a similar manner as BH3 peptide. Our results provide insights into the novel molecular recognition by Bcl-XL with p53.
Identification of a Novel Function of CX-4945 as a Splicing Regulator
Hyeongki Kim, Kwangman Choi, Hyunju Kang, So-Young Lee, Seung-Wook Chi, Min-Sung Lee, Jaehyoung Song, Donghwa Im, Yura Choi, Sungchan Cho
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0094978
Abstract: Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that CX-4945, a previously well-characterized inhibitor of casein kinase 2 (CK2) and a molecule currently in clinical trials (Phase II) for cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that CX-4945 potently inhibits the Cdc2-like kinases (Clks) in vitro and in turn, leads to suppression of the phosphorylation of serine/arginine-rich (SR) proteins in mammalian cells. Surprisingly, the overall efficacy of CX-4945 on Clks (IC50 = 3–90 nM) was stronger than that of TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by CX-4945 in an ATP-competitive manner. Our research revealed an unexpected activity of the drug candidate CX-4945 as a potent splicing modulator and also suggested a potential application for therapy of diseases caused by abnormal splicing.
Gender-Specific Metabolomic Profiling of Obesity in Leptin-Deficient ob/ob Mice by 1H NMR Spectroscopy
Eun-Young Won, Mi-Kyung Yoon, Sang-Woo Kim, Youngae Jung, Hyun-Whee Bae, Daeyoup Lee, Sung Goo Park, Chul-Ho Lee, Geum-Sook Hwang, Seung-Wook Chi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0075998
Abstract: Despite the numerous metabolic studies on obesity, gender bias in obesity has rarely been investigated. Here, we report the metabolomic analysis of obesity by using leptin-deficient ob/ob mice based on the gender. Metabolomic analyses of urine and serum from ob/ob mice compared with those from C57BL/6J lean mice, based on the 1H NMR spectroscopy in combination with multivariate statistical analysis, revealed clear metabolic differences between obese and lean mice. We also identified 48 urine and 22 serum metabolites that were statistically significantly altered in obese mice compared to lean controls. These metabolites are involved in amino acid metabolism (leucine, alanine, ariginine, lysine, and methionine), tricarbocylic acid cycle and glucose metabolism (pyruvate, citrate, glycolate, acetoacetate, and acetone), lipid metabolism (cholesterol and carnitine), creatine metabolism (creatine and creatinine), and gut-microbiome-derived metabolism (choline, TMAO, hippurate, p-cresol, isobutyrate, 2-hydroxyisobutyrate, methylamine, and trigonelline). Notably, our metabolomic studies showed distinct gender variations. The obese male mice metabolism was specifically associated with insulin signaling, whereas the obese female mice metabolism was associated with lipid metabolism. Taken together, our study identifies the biomarker signature for obesity in ob/ob mice and provides biochemical insights into the metabolic alteration in obesity based on gender.
Dual-Specificity Phosphatase 10 Controls Brown Adipocyte Differentiation by Modulating the Phosphorylation of P38 Mitogen-Activated Protein Kinase
Hye-Ryung Choi, Won Kon Kim, Eun Young Kim, Baek Soo Han, Jeong-Ki Min, Seung-Wook Chi, Sung Goo Park, Kwang-Hee Bae, Sang Chul Lee
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072340
Abstract: Background Brown adipocytes play an important role in regulating the balance of energy, and as such, there is a strong correlation between obesity and the amount of brown adipose tissue. Although the molecular mechanism underlying white adipocyte differentiation has been well characterized, brown adipocyte differentiation has not been studied extensively. Here, we investigate the potential role of dual-specificity phosphatase 10 (DUSP10) in brown adipocyte differentiation using primary brown preadipocytes. Methods and Results The expression of DUSP10 increased continuously after the brown adipocyte differentiation of mouse primary brown preadipocytes, whereas the phosphorylation of p38 was significantly upregulated at an early stage of differentiation followed by steep downregulation. The overexpression of DUSP10 induced a decrease in the level of p38 phosphorylation, resulting in lower lipid accumulation than that in cells overexpressing the inactive mutant DUSP10. The expression levels of several brown adipocyte markers such as PGC-1α, UCP1, and PRDM16 were also significantly reduced upon the ectopic expression of DUSP10. Furthermore, decreased mitochondrial DNA content was detected in cells expressing DUSP10. The results obtained upon treatment with the p38 inhibitor, SB203580, clearly indicated that the phosphorylation of p38 at an early stage is important in brown adipocyte differentiation. The effect of the p38 inhibitor was partially recovered by DUSP10 knockdown using RNAi. Conclusions These results suggest that p38 phosphorylation is controlled by DUSP10 expression. Furthermore, p38 phosphorylation at an early stage is critical in brown adipocyte differentiation. Thus, the regulation of DUSP10 activity affects the efficiency of brown adipogenesis. Consequently, DUSP10 can be used as a novel target protein for the regulation of obesity.
Inhibition of Proteasomal Degradation of Rpn4 Impairs Nonhomologous End-Joining Repair of DNA Double-Strand Breaks
Donghong Ju,Xiaogang Wang,Seung-Wook Ha,Jiejun Fu,Youming Xie
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009877
Abstract: The proteasome homeostasis in Saccharomyces cerevisiae is regulated by a negative feedback circuit in which the transcription factor Rpn4 induces the proteasome genes and is rapidly degraded by the assembled proteasome. The integrity of the Rpn4-proteasome feedback loop is critical for cell viability under stressed conditions. We have demonstrated that inhibition of Rpn4 degradation sensitizes cells to DNA damage, particularly in response to high doses of DNA damaging agents. The underlying mechanism, however, remains unclear.
Downregulation of OPA3 Is Responsible for Transforming Growth Factor-β-Induced Mitochondrial Elongation and F-Actin Rearrangement in Retinal Pigment Epithelial ARPE-19 Cells
Seung-Wook Ryu, Jonghee Yoon, Nambin Yim, Kyungsun Choi, Chulhee Choi
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0063495
Abstract: Transforming growth factor-β signaling is known to be a key signaling pathway in the induction of epithelial–mesenchymal transition. However, the mechanism of TGF-β signaling in the modulation of EMT remains unclear. In this study, we found that TGF-β treatment resulted in elongation of mitochondria accompanied by induction of N-cadherin, vimentin, and F-actin in retinal pigment epithelial cells. Moreover, OPA3, which plays a crucial role in mitochondrial dynamics, was downregulated following TGF-β treatment. Suppression of TGF-β signaling using Smad2 siRNA prevented loss of OPA3 induced by TGF-β. Knockdown of OPA3 by siRNA and inducible shRNA significantly increased stress fiber levels, cell length, cell migration and mitochondrial elongation. In contrast, forced expression of OPA3 in ARPE-19 cells inhibited F-actin rearrangement and induced mitochondrial fragmentation. We also showed that Drp1 depletion increased cell length and induced rearrangement of F-actin. Depletion of Mfn1 blocked the increase in cell length during TGF-β-mediated EMT. These results collectively substantiate the involvement of mitochondrial dynamics in TGF-β-induced EMT.
Mutant Ubiquitin UBB+1 Induces Mitochondrial Fusion by Destabilizing Mitochondrial Fission-Specific Proteins and Confers Resistance to Oxidative Stress-Induced Cell Death in Astrocytic Cells
Nambin Yim, Seung-Wook Ryu, Eun Chun Han, Jonghee Yoon, Kyungsun Choi, Chulhee Choi
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0099937
Abstract: Mutant ubiquitin UBB+1 is observed in a variety of aging-related neurodegenerative diseases and acts as a potent inhibitor of the ubiquitin proteasome system (UPS). In the present study, we investigated the relationship between impaired UPS (using ectopic expression of UBB+1) and mitochondrial dynamics in astrocytes, which are the most abundant glial cells in the central nervous system. Immunocytochemistry and fluorescence recovery after photobleaching revealed that ectopic expression of UBB+1 induced mitochondrial elongation. We further demonstrated that overexpression of UBB+1 destabilized mitochondrial fission-specific proteins including Drp1, Fis1, and OPA3, but not the mitochondrial fusion-specific proteins Mfn1, Mfn2, and OPA1. The reduction in mitochondrial fission-specific proteins by UBB+1 was prevented by inhibiting the 26 S proteasome using chemical inhibitors, including MG132, lactacystin and epoxomicin. We then assessed the involvement of proteases that target mitochondrial proteins by using various protease inhibitors. Finally, we confirmed that either overexpression of UBB+1 or inhibiting the proteasome can protect astrocytic cells from H2O2-induced cell death compared with control cells. Our results suggest that UBB+1 destabilizes mitochondrial fission-specific proteins, leading to mitochondrial fusion and the subsequent resistance to oxidative stress. We therefore propose a protective role of UBB+1 overexpression or the proteasome inhibition in astrocytes in degenerative brains.
GSE Is a Maternal Factor Involved in Active DNA Demethylation in Zygotes
Yuki Hatanaka, Natsumi Shimizu, Satoshi Nishikawa, Mikiko Tokoro, Seung-Wook Shin, Takuji Nishihara, Tomoko Amano, Masayuki Anzai, Hiromi Kato, Tasuku Mitani, Yoshihiko Hosoi, Satoshi Kishigami, Kazuya Matsumoto
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060205
Abstract: After fertilization, the sperm and oocyte genomes undergo extensive epigenetic reprogramming to form a totipotent zygote. The dynamic epigenetic changes during early embryo development primarily involve DNA methylation and demethylation. We have previously identified Gse (gonad-specific expression gene) to be expressed specifically in germ cells and early embryos. Its encoded protein GSE is predominantly localized in the nuclei of cells from the zygote to blastocyst stages, suggesting possible roles in the epigenetic changes occurring during early embryo development. Here, we report the involvement of GSE in epigenetic reprogramming of the paternal genome during mouse zygote development. Preferential binding of GSE to the paternal chromatin was observed from pronuclear stage 2 (PN2) onward. A knockdown of GSE by antisense RNA in oocytes produced no apparent effect on the first and second cell cycles in preimplantation embryos, but caused a significant reduction in the loss of 5-methylcytosine (5 mC) and the accumulation of 5-hydroxymethylcytosine (5 hmC) in the paternal pronucleus. Furthermore, DNA methylation levels in CpG sites of LINE1 transposable elements, Lemd1, Nanog and the upstream regulatory region of the Oct4 (also known as Pou5f1) gene were clearly increased in GSE-knockdown zygotes at mid-pronuclear stages (PN3-4), but the imprinted H19-differential methylated region was not affected. Importantly, DNA immunoprecipitation of 5 mC and 5 hmC also indicates that knockdown of GSE in zygotes resulted in a significant reduction of the conversion of 5 mC to 5 hmC on LINE1. Therefore, our results suggest an important role of maternal GSE for mediating active DNA demethylation in the zygote.
Solubility enhancement of aggregation-prone heterologous proteins by fusion expression using stress-responsive Escherichia coli protein, RpoS
Jin-Seung Park, Kyung-Yeon Han, Jong-Ho Lee, Jong-Am Song, Keum-Young Ahn, Hyuk-Seong Seo, Sang-Jun Sim, Seung-Wook Kim, Jeewon Lee
BMC Biotechnology , 2008, DOI: 10.1186/1472-6750-8-15
Abstract: We analyzed the Escherichia coli proteome response to the exogenous stress of guanidine hydrochloride using 2-dimensional gel electrophoresis and found that RpoS (RNA polymerase sigma factor) was significantly stress responsive. While under the stress condition the total number of soluble proteins decreased by about 7 %, but a 6-fold increase in the level of RpoS was observed, indicating that RpoS is a stress-induced protein. As an N-terminus fusion expression partner, RpoS increased significantly the solubility of many aggregation-prone heterologous proteins in E. coli cytoplasm, indicating that RpoS is a very effective solubility enhancer for the synthesis of many recombinant proteins. RpoS was also well suited for the production of a biologically active fusion mutant of Pseudomonas putida cutinase.RpoS is highly effective as a strong solubility enhancer for aggregation-prone heterologous proteins when it is used as a fusion expression partner in an E. coli expression system. The results of these findings may, therefore, be useful in the production of other biologically active industrial enzymes, as successfully demonstrated by cutinase.Escherichia coli have been widely used as a host to produce valuable commercial, industrial, and therapeutic proteins. There are several disadvantages with this system, however, especially for the expression of eukaryotic proteins. For example, when randomly selected 2,078 full-length genes of Caenorhabditis elegans were expressed in E. coli cytoplasm, only 11% of genes yielded significant amounts of soluble material [1]. Several different approaches have been taken to resolve the solubility problem in the past and include (1) truncation of long multi-domain proteins into short and separate domains [2] ; (2) co-expression of molecular chaperones or foldases [3]; (3) enabled secretion to the periplasm where disulfide bonds can be properly formed with the help of an oxidative environment and Dsb protein families [4]; (4) co-expressio
Simplified Large-Scale Refolding, Purification, and Characterization of Recombinant Human Granulocyte-Colony Stimulating Factor in Escherichia coli
Chang Kyu Kim, Chi Ho Lee, Seung-Bae Lee, Jae-Wook Oh
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080109
Abstract: Granulocyte-colony stimulating factor (G-CSF) is a pleiotropic cytokine that stimulates the development of committed hematopoietic progenitor cells and enhances the functional activity of mature cells. Here, we report a simplified method for fed-batch culture as well as the purification of recombinant human (rh) G-CSF. The new system for rhG-CSF purification was performed using not only temperature shift strategy without isopropyl-l-thio-β-d-galactoside (IPTG) induction but also the purification method by a single step of prep-HPLC after the pH precipitation of the refolded samples. Through these processes, the final cell density and overall yield of homogenous rhG-CSF were obtained 42.8 g as dry cell weights, 1.75 g as purified active proteins, from 1 L culture broth, respectively. The purity of rhG-CSF was finally 99% since the isoforms of rhG-CSF could be separated through the prep-HPLC step. The result of biological activity indicated that purified rhG-CSF has a similar profile to the World Health Organization (WHO) 2nd International Standard for G-CSF. Taken together, our results demonstrate that the simple purification through a single step of prep-HPLC may be valuable for the industrial-scale production of biologically active proteins.
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