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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Korean Society for Biochemistry and Molecular Biology
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Volume & Issues
Volume 41, Issue 12 - Dec 2008
Volume 41, Issue 11 - Nov 2008
Volume 41, Issue 10 - Oct 2008
Volume 41, Issue 9 - Sep 2008
Volume 41, Issue 8 - Aug 2008
Volume 41, Issue 7 - Jul 2008
Volume 41, Issue 6 - Jun 2008
Volume 41, Issue 5 - May 2008
Volume 41, Issue 4 - Apr 2008
Volume 41, Issue 3 - Mar 2008
Volume 41, Issue 2 - Feb 2008
Volume 41, Issue 1 - Jan 2008
Selecting the target year
Evaluation of proteomic strategies for analyzing ubiquitinated proteins
Peng, Jun Min ;
BMB Reports , volume 41, issue 3, 2008, Pages 177~183
DOI : 10.5483/BMBRep.2008.41.3.177
Ubiquitin is an essential, highly-conserved small regulatory protein in eukaryotic cells. It covalently modifies a wide variety of targeted proteins in the forms of monomer and polymers, altering the conformation and binding properties of the proteins and thus regulating proteasomal delivery, protein activities and localization. Mass spectrometry has emerged as an indispensable tool for in-depth characterization of protein ubiquitination. Ubiquitinated proteins in cell lysates are usually enriched by affinity chromatography and subsequently analyzed by mass spectrometry for identification and quantification. Ubiquitin-conjugated amino acid residues can be determined by unique mass shift caused by the modification. Moreover, the complex structure of polyubiquitin chains on substrates can be dissected by bottom-up and middle-down mass spectrometric approaches, revealing potential novel functions of polyubiquitin linkages. Here I review the advances and caveats of these strategies, emphasizing caution in the validation of ubiquitinated proteins and in the interpretation of raw data.
From proteomics toward systems biology: integration of different types of proteomics data into network models
Rho, Sang-Chul ; You, Sung-Yong ; Kim, Yong-Soo ; Hwang, Dae-Hee ;
BMB Reports , volume 41, issue 3, 2008, Pages 184~193
DOI : 10.5483/BMBRep.2008.41.3.184
Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems biology investigates such systems by producing comprehensive global data that represent different levels of biological information, i.e., at the DNA, mRNA, protein, or metabolite levels, and by integrating this data into network models that generate coherent hypotheses for given biological situations. This review presents a systems biology framework, called the 'Integrative Proteomics Data Analysis Pipeline' (IPDAP), which generates mechanistic hypotheses from network models reconstructed by integrating diverse types of proteomic data generated by mass spectrometry-based proteomic analyses. The devised framework includes a serial set of computational and network analysis tools. Here, we demonstrate its functionalities by applying these tools to several conceptual examples.
Nitrosative protein tyrosine modifications: biochemistry and functional significance
Yeo, Woon-Seok ; Lee, Soo-Jae ; Lee, Jung-Rok ; Kim, Kwang-Pyo ;
BMB Reports , volume 41, issue 3, 2008, Pages 194~203
DOI : 10.5483/BMBRep.2008.41.3.194
Nitrosative modifications regulate cellular signal transduction and pathogenesis of inflammatory responses and neuro-degenerative diseases. Protein tyrosine nitration is a biomarker of oxidative stress and also influences protein structure and function. Recent advances in mass spectrometry have made it possible to identify modified proteins and specific modified amino acid residues. For analysis of nitrated peptides with low yields or only a subset of peptides, affinity 'tags' can be bait for 'fishing out' target analytes from complex mixtures. These tagged peptides are then extracted to a solid phase, followed by mass analysis. In this review, we focus on protein tyrosine modifications caused by nitrosative stresses and proteomic methods for selective enrichment and identification of nitrosative protein modifications.
Molecular characterization of glutathione peroxidase gene from the liver of silver carp, bighead carp and grass carp
Li, Guang-Zhao ; Liang, Xu-Fang ; Yao, Wei ; Liao, Wan-Qin ; Zhu, Wei-Feng ;
BMB Reports , volume 41, issue 3, 2008, Pages 204~209
DOI : 10.5483/BMBRep.2008.41.3.204
The cDNAs encoding glutathione peroxidase (GPx) were cloned and sequenced from the liver of three Chinese carps with different tolerance to hepatotoxic microcystins, phyto-planktivorous silver carp (Hypophthalmichthys molitrix) and bighead carp (Aristichthys nobilis), and herbivorous grass carp (Ctenopharyngodon idellus). Using genome walker method, a 750 bp 5'-flanking region of the silver carp GPx gene was obtained, and several potential regulatory elements were identified in the promoter region of the GPx gene. The silver carp GPx gene was widely expressed in all tissues examined. Despite phylogenetic analysis, assigning this newly described carp GPx to the group of mammalian GPx2, the carp GPx seems more similar to GPx1 from a physiological point of view. The constitutive expression pattern of the three carp liver GPx gene, shows a positive relationship with their tolerance to microcystins.
CSE1L/CAS, a microtubule-associated protein, inhibits taxol (paclitaxel)-induced apoptosis but enhances cancer cell apoptosis induced by various chemotherapeutic drugs
Liao, Ching-Fong ; Luo, Shue-Fen ; Shen, Tzu-Yun ; Lin, Chin-Huang ; Chien, Jung-Tsun ; Du, Shin-Yi ; Jiang, Ming-Chung ;
BMB Reports , volume 41, issue 3, 2008, Pages 210~216
DOI : 10.5483/BMBRep.2008.41.3.210
CSE1L/CAS, a microtubule-associated, cellular apoptosis susceptibility protein, is highly expressed in various cancers. Microtubules are the target of paclitaxel-induced apoptosis. We studied the effects of increased or reduced CAS expression on cancer cell apoptosis induced by chemotherapeutic drugs including paclitaxel. Our results showed that CAS overexpression enhanced apoptosis induced by doxorubicin, 5-fluorour-acil, cisplatin, and tamoxifen, but inhibited paclitaxel-induced apoptosis of cancer cells. Reductions in CAS produced opposite results. CAS overexpression enhanced p53 accumulation induced by doxorubicin, 5-fluorouracil, cisplatin, tamoxifen, and etoposide. CAS was associated with
-tubulin and enhanced the association between
-tubulin. Paclitaxel can induce G2/M phase cell cycle arrest and microtubule aster formation during apoptosis induction, but CAS overexpression reduced paclitaxel-induced G2/M phase cell cycle arrest and microtubule aster formation. Our results indicate that CAS may play an important role in regulating the cytotoxicities of chemotherapeutic drugs used in cancer chemotherapy against cancer cells.
2-D graphical representation of protein sequences and its application to coronavirus phylogeny
Li, Chun ; Xing, Lili ; Wang, Xin ;
BMB Reports , volume 41, issue 3, 2008, Pages 217~222
DOI : 10.5483/BMBRep.2008.41.3.217
Based on a five-letter model of the 20 amino acids, we propose a new 2-D graphical representation of protein sequence. Then we transform the 2-D graphical representation into a numerical characterization that will facilitate quantitative comparisons of protein sequences. As an application, we construct the phylogenetic tree of 56 coronavirus spike proteins. The resulting tree agrees well with the established taxonomic groups.
The bimodal regulation of vascular function by superoxide anion: role of endothelium
Demirci, Buket ; McKeown, Pascal P. ; Bayraktutan DVM, Ulvi ;
BMB Reports , volume 41, issue 3, 2008, Pages 223~229
DOI : 10.5483/BMBRep.2008.41.3.223
Reactive oxygen species (ROS) are implicated in vascular homeostasis. This study investigated whether
, the foundation molecule of all ROS, regulates vasomotor function. Hence, vascular reactivity was measured using rat thoracic aortas exposed to an
generator (pyrogallol) which dose-dependently regulated both
-adrenergic agonist-mediated contractility to phenylephrine and endothelium-dependent relaxations to acetylcholine. Pyrogallol improved and attenuated responses to acetylcholine at its lower (10 nM - 1
) and higher (10 - 100
) concentrations, respectively while producing the inverse effects with phenylephrine. The endothelial inactivation by L-NAME abolished acetylcholine-induced vasodilatations but increased phenylephrine and KCl-induced vasoconstrictions regardless of the pyrogallol dose used. Relaxant responses to sodium nitroprusside, a nitric oxide donor, were not affected by pyrogallol. Other ROS i.e. peroxynitrite and
that may be produced during experiments did not alter vascular functions. These findings suggest that the nature of
-evoked vascular function is determined by its local concentration and the presence of a functional endothelium.
The novel gene LRP15 is regulated by DNA methylation and confers increased efficiency of DNA repair of ultraviolet-induced DNA damage
Xu, Zhou-Min ; Gao, Wei-Ran ; Mei, Qi ; Chen, Jian ; Lu, Jing ;
BMB Reports , volume 41, issue 3, 2008, Pages 230~235
DOI : 10.5483/BMBRep.2008.41.3.230
LRP15 is a novel gene cloned from lymphocytic cells, and its function is still unknown. Bioinformatic data showed that LRP15 might be regulated by DNA methylation and had an important role in DNA repair. In this study, we investigate whether the expression of LRP15 is regulated by DNA methylation, and whether overexpression of LRP15 increases efficiency of DNA repair of UV-induced DNA damage in HeLa cells. The results showed (1) the promoter of LRP15 was hypermethylated in HeLa cells, resulting a silence of its expression. Gene expression was restored by a demethylating agent, 5-aza-2'-deoxycytidine, but not by a histone deacetylase inhibitor, trichostatin A; (2) overexpression of LRP15 inhibited HeLa cell proliferation, and the numbers of cells in the G2/M phase of the cell cycle in cells transfected with LRP15 increased about 10% compared with controls; (3) cyclin B1 level was much lower in cells overexpressing LRP15 than in control cells; and (4) after exposure to UV radiation, the LRP15-positive cells showed shorter comet tails compared with the LRP15-negative cells. From these results we conclude that the expression of LRP15 is controlled by methylation in its promoter in HeLa cells, and LRP15 confers resistance to UV damage and accelerates the DNA repair rate.
Antioxidant potential of silk protein sericin against hydrogen peroxide-induced oxidative stress in skin fibroblasts
Dash, Rupesh ; Acharya, Chitrangada ; Bindu, P.C. ; Kundu, S.C. ;
BMB Reports , volume 41, issue 3, 2008, Pages 236~241
DOI : 10.5483/BMBRep.2008.41.3.236
The antioxidant potential of silk protein sericin from the non-mulberry tropical tasar silkworm Antheraea mylitta cocoon has been assessed and compared with that of the mulberry silkworm, Bombyx mori. Skin fibroblast cell line (AH927) challenged with hydrogen peroxide served as the positive control for the experiment. Our results showed that the sericin obtained from tasar cocoons offers protection against oxidative stress and cell viability is restored to that of control on pre-incubation with the sericin. Fibroblasts pre-incubated with non-mulberry sericin had significantly lower levels of catalase; lactate dehydrogenase and malondialdehyde activity when compared to untreated ones. This report indicates that the silk protein sericin from the non-mulberry tropical tasar silkworm, A. mylitta can serve as a valuable antioxidant.
Memory-improving effect of formulation-MSS by activation of hippocampal MAPK/ERK signaling pathway in rats
Kim, Sang-Won ; Ha, Na-Young ; Kim, Kyung-In ; Park, Jin-Kyu ; Lee, Yong-Heun ;
BMB Reports , volume 41, issue 3, 2008, Pages 242~247
DOI : 10.5483/BMBRep.2008.41.3.242
MSS, a comprising mixture of maesil (Prunus mume Sieb. et Zucc) concentrate, disodium succinate and Span80 (3.6 : 4.6 : 1 ratio) showed a significant improvement of memory when daily administered (460 mg/kg day, p.o.) into the normal rats for 3 weeks. During the spatial learning of 4 days in Morris water maze test, both working memory and short-term working memory index were significantly increased when compared to untreated controls. We investigated a molecular signal transduction mechanism of MSS on the behaviors of spatial learning and memory. MSS treatment increased hippocampal mRNA levels of NR2B and TrkB without changes of NR1, NR2A, ERK1, ERK2 and CREB. However, the protein levels of pERK/ERK and pCREB/CREB were all significantly increased to
times. These results suggest that the improving effect of spatial memory for MSS is linked to MAPK/ERK signaling pathway that ends up in the phosphorylation of CREB through TrkB and/or NR2B of NMDA receptor.
A pheromone mutant of Schizosaccharomyces pombe displays nucleolar fragmentation
Jun, Jai-Hyun ; Kim, Dae-Myung ;
BMB Reports , volume 41, issue 3, 2008, Pages 248~253
DOI : 10.5483/BMBRep.2008.41.3.248
Stresses and nutritional starvation are two main external signals for the induction of sex pheromones in the fission yeast Schizosaccharomyces pombe. In an attempt to identify the components involved in transduction of starvation signals, we screened 135 temperature-sensitive (ts) mutants and isolated 6 mutants that induced the pheromone even in the presence of a nitrogen source. These mutants exhibited two distict induction phenotypes: pheromone induction at restrictive but not at permissive temperatures; and pheromone induction at both permissive and restrictive temperatures. The times required for the maximum pheromone induction at the restrictive temperature differed slightly in each mutant. In addition to the pheromone induction phenotype, the ts243 and ts304 mutants exhibited cell-division-cycle defects. The ts304 mutant cells showed an abnormal cytoplasmic DAPI staining pattern. The nucleolus of this mutant seemed to be fragmented, a phenomenon which is typically observed in aged yeast cells. The result of our genetic analysis indicated that the pheromone induction mutants belonged to 6 separate complementation groups. We designated these mutants pws1 to pws6.
Purification and characterization of hepatic lipase from Todarodes pacificus
Park, Jong-Won ; Cho, Soon-Yeong ; Choi, Suk-Jung ;
BMB Reports , volume 41, issue 3, 2008, Pages 254~258
DOI : 10.5483/BMBRep.2008.41.3.254
Lipase was purified from squid (Todarodes pacificus) liver in an attempt to investigate the possibility of applying the enzyme for biotechnological applications. Crude extract of squid liver was initially fractionated by the batch type ion exchange chromatography. The fraction containing lipase activity was further purified with an octyl-Sepharose column. Finally, lipase was purified by eluting active protein from a non-dissociating polyacrylamide gel after zymographic analysis. Molecular weight of the purified enzyme was determined to be 27 kDa by SDS-polyacrylamide gel electrophoresis. The enzyme showed the highest activity at a temperature range of
and at pH 8.0. The activity was almost completely inhibited at 1 mM concentration of
ion. Partial amino acid sequence of the enzyme was also determined.
Molecular cloning of peroxidase cDNAs from dehydration-treated fibrous roots of sweetpotato and their differential expression in response to stress
Kim, Yun-Hee ; Yang, Kyoung-Sil ; Kim, Cha-Young ; Ryu, Sun-Hwa ; Song, Wan-Keun ; Kwon, Suk-Yoon ; Lee, Haeng-Soon ; Bang, Jae-Wook ; Kwak, Sang-Soo ;
BMB Reports , volume 41, issue 3, 2008, Pages 259~265
DOI : 10.5483/BMBRep.2008.41.3.259
Three peroxidase (POD) cDNAs were isolated from dehydration-treated fibrous roots of sweetpotato (Ipomoea batatas) plant via the screening of a cDNA library, and their expressions were assessed to characterize functions of each POD in relation to environmental stress. Three PODs were divided into two groups, designated the basic PODs (swpb4, swpb5) and the anionic PODs (swpa7), on the basis of the pI values of mature proteins. Fluorescence microscope analysis indicated that three PODs are secreted into the extracellular space. RT-PCR analysis revealed that POD genes have diverse expression patterns in a variety of plant tissues. Swpb4 was abundantly expressed in stem tissues, whereas the expression levels of swpb5 and swpa7 transcripts were high in fibrous and thick pigmented roots. Swpb4 and swpa7 showed abundant expression levels in suspension cultured cells. Three POD genes responded differently in the leaf and fibrous roots in response to a variety of stresses including dehydration, temperature stress, stress-associated chemicals, and pathogenic bacteria.