• KSBB Journal
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• v.16 no.2
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• pp.99-106
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• 2001

Proteomics research includes identification and quantitation of single protein and/or protein complex, profiling of protein expression changes in response to biological perturbations, characterization of protein functions and interactions, and elucidation the linkage between proteins and diseases. In this review paper, recent developments in the basic technologies involved in the proteomics research such as 2-dimensional PAGE and mass spectrometry are discussed. Also, the application areas of proteomics technology such as protein expression mapping and cell map proteomics are introduced with the focus on new drug development.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.13
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• pp.5325-5330
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• 2014

Background: Chronic myelocytic leukemia is a disease that threatens both adults and children. Great progress has been achieved in treatment but protein-protein interaction networks underlining chronic myelocytic leukemia are less known. Objective: To develop a protein-protein interaction network for chronic myelocytic leukemia based on gene expression and to predict biological pathways underlying molecular complexes in the network. Materials and Methods: Genes involved in chronic myelocytic leukemia were selected from OMIM database. Literature mining was performed by Agilent Literature Search plugin and a protein-protein interaction network of chronic myelocytic leukemia was established by Cytoscape. The molecular complexes in the network were detected by Clusterviz plugin and pathway enrichment of molecular complexes were performed by DAVID online. Results and Discussion: There are seventy-nine chronic myelocytic leukemia genes in the Mendelian Inheritance In Man Database. The protein-protein interaction network of chronic myelocytic leukemia contained 638 nodes, 1830 edges and perhaps 5 molecular complexes. Among them, complex 1 is involved in pathways that are related to cytokine secretion, cytokine-receptor binding, cytokine receptor signaling, while complex 3 is related to biological behavior of tumors which can provide the bioinformatic foundation for further understanding the mechanisms of chronic myelocytic leukemia.

• Applied Microscopy
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• v.30 no.2
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• pp.185-191
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• 2000

An unusually large protein complex was found in the cytosol of the hyperthmophilic archaeon. Thermococcus profundus. The purified protein was shown to be a homomultimer of 93 kDa subunit (P93 complex). The complex is extremely heat stable. During 12 hrs incubation with SDS (final concentration 1%) at $85^{\circ}C$, no changed structure could be observed. Electron image analysis of negatively stained showed that the complex has a single, stable characteristic view and a well-preserved core with threefold rotational symmetry. The periphery of the assembly is composed of a nebulose, possibly flexible, component. Based on the projected structure suggest the P93 complex from T. profundus is composed 24 homomultimer.

• Journal of Microbiology and Biotechnology
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• v.9 no.5
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• pp.604-612
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• 1999

A puc-deleted cell of Rhodobacter sphaeroides grows with a doubling time longer than 160 h under light-limiting photoheterotrophic (3 Watts [W]/㎡) conditions due to an absence of the peripheral light-harvesting B800-850 complex. A spontaneous fast-growing mutant, R. sphaeroides SK101, was isolated from the puc-deleted cells cultured photoheterotrophically at 3 W/㎡. This mutant grew with an approximately 40-h doubling time. The growth of the mutant, however, was indistinguishable from its parental strain during photoheterotrophic growth at 10 W/㎡ as well as during aerobic growth. The membrane of SK101 grown aerobically did not reveal the presence of any spectral complex, while the amounts of the B875 complex and photosynthetic pigments of SK101 grown anaerobiclly in the dark with dimethylsulfoxide (DMSO) were the same as those of the parental cell. These results indicate that the oxygen control of the photosynthetic complex formation remained unaltered in the mutant. The B875 complex of SK101 under light-limiting conditions was elevated by 20％ to 30％ compared with that of the parental cell, which reflected the parallel increase of the bacteriochlorophyll and carotenoid contents of the mutant. When the puc was restored in SK101, the B875 complex level remained unchanged, but that of the B800-850 complex increased. The mutated phenotype of SK101 was complemented with orfQ encoding a putative bacteriochlorophyll-mobilizing protein. Accordingly, it is proposed that the mutated OrfQ of SK101 should have an altered affinity towards the assembly factor specific to the most peripheral light-harvesting complex, which could be either the B875 or the B800-850 complex.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.9
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• pp.1261-1267
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• 2003

We have investigated whether HspBP1, a Hsp70 binding protein, could have effect on the assembly of the bovine progesterone receptor (bPR) with a chaperone complex consisting of bovine Hsp90 (bHsp90), bovine Hsp70 (bHsp70), Hop, Ydj-1, and p23. The bPR, isolated in its native conformation, loses its function to interact with progesterone hormone in the absence of this protein complex. However, in the presence of bHsp90, bHsp70, Hop, p23 and Ydj-1, its function could be restored in vitro. Our findings here indicate that the inclusion of HspBP1 to five-protein system prevented the proper assembly of progesterone receptor-chaperone complex and induce the loss of bPR ability to interact with hormone. Immunoprecipitation assays of bPR with HspBP1 show that the presence of HspBP1 did not have any effect on the assembly of Ydj-1 and bHsp70 with the progesterone receptor. However, further assembly of Hsp90, Hop and p23 was completely prevented and the function of the bPR was lost. In vitro competition and protein folding assays indicated that the binding of HspBP1 to bHsp70 prevented the ternary complex formation of bHsp70, bHsp90, and Hop. These results indicate that HspBP1 is a negative regulator of the assembly of Hsp90, Hop and Hsp70, and thus, prevent the proper maturation of unliganded bPR with chaperones assembly system.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.325-329
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• 2018

Thp1/PCID2, PCI domain-containing protein, is a component of the evolutionally conserved TREX-2 complex linking mRNA transcription and export. In fission yeast, Schizosaccharomyces pombe, the pci2 (SPBC1105.07c) gene encodes a PCI domain-containing protein that is predicted as a fission yeast orthologue of Thp1 (in budding yeast)/PCID2 (in human). Repression of pci2 expression inhibited both growth and mRNA export. And over-expression of pci2 also exhibited growth retardation with slight accumulation of $poly(A)^+$ RNA in the nucleus. Moreover, yeast two-hybrid and co-immunoprecipitation analysis showed that the Pci2 protein physically interacted with Sac3 and Dss1, which are members of TREX-2 complex. These observations support that the S. pombe Pci2 protein, as a component of TREX-2 complex, is implicated in mRNA export.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.197-201
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• 2004

A 2-D gel protein analysis of Lactobacillus reuteri ATCC 55739 produced spots corresponding to subunits of the pyruvate dehydrogenase complex, as identified by N-terminal protein sequencing. Oligonucleotide probes specific for the subunits of the pyruvate dehydrogenase complex were synthesized ,md used to screen a L. reuteri genomic library to clone the structural genes. Two positive clones were isolated and identified as having the same 2.2 kb insert. A pdhB encoding the $\beta$-subunit of El subunit (pyruvate dehydrogenase component) of the pyruvate dehydrogenase complex was located in the middle of the insert. Furthermore, a 5' truncated pdhA encoding the $\alpha$-subunit of the E1 subunit and a 3' truncated pdhC encoding the E2 subunit (dihydrolipoamide acetyltransferase) were also located upstream and downstream of the pdhB, respectively.

• Natural Product Sciences
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• v.5 no.3
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• pp.148-150
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• 1999

Seed lipids and proteins of Crotalaria juncea L were analyzed for fatty acids and amino acids respectively. Gas chromatographic analysis of the oil gave palmitic acid (16.01%), stearic acid (7.29%), oleic acid (14.41%), linoleic acid (54.44%) and linolenic acid (7.86%). The defatted seed cake contained all the essential amino acids except methionine and six non-essential amino acids.

• BMB Reports
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• v.42 no.12
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• pp.817-822
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• 2009

Type-1 phosphatase (PP-1) was assessed in foot muscle (FM) and hepatopancreas (HP) of estivating (EST) Otala lactea. Snail PP-1 displayed several conserved traits, including sensitivity to inhibitors, substrate affinity, and reduction in size to a 39 kDa catalytic subunit (PP-1c). During EST, PP-1 activity in FM and HP crude extracts was reduced, though kinetics and protein levels of purified PP-1c isoforms were not altered. PP-1c protein levels increased and decreased in nuclear and glycogen-associated fractions, respectively, during EST. Gel filtration determined that a 257 kDa low $K_m$ PP-1$\alpha$ complex decreased during estivation whereas a 76 kDa high $K_m$ complex increased in EST. Western blotting confirmed that the 76 kDa protein consisted of PP-1$\alpha$ and nuclear inhibitor of PP-1 (NIPP-1). A suppression of PP-1 activity factors in the overall metabolic rate depression in estivating snails and the mechanism is mediated through altered cellular localization and interaction with binding partners.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.102-108
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• 2016

With the rapid increase of data on protein-protein interactions, the need for delineating the 3D structures of huge protein complexes has increased. The protocols for determining nuclear magnetic resonance (NMR) structure can be applied to modeling complex structures coupled with sparse experimental restraints. In this report, I suggest the use of multiple rigid bodies for improving the efficiency of NMR-assisted structure modeling of huge complexes using CYANA. By preparing a region of known structure as a new type of residue that has no torsion angle, one can facilitate the search of the conformational spaces. This method has a distinct advantage over the rigidification of a region with synthetic distance restraints, particularly for the calculation of huge molecules. I have demonstrated the idea with calculations of decaubiquitins that are linked via Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, or Lys63, or head to tail. Here, the ubiquitin region consisting of residues 1-70 was treated as a rigid body with a new residue. The efficiency of the calculation was further demonstrated in Lys48-linked decaubiquitin with ambiguous distance restraints. The approach can be readily extended to either protein-protein complexes or large proteins consisting of several domains.