• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.133-138
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• 2003

The prediction of protein secondary structure has been an important bioinformatics tool that is an essential component of the template-based protein tertiary structure prediction process. It has been known that the predicted secondary structure information improves both the fold recognition performance and the alignment accuracy. In this paper, we describe several novel ideas that may improve the prediction accuracy. The main idea is motivated by an observation that the protein's structural information, especially when it is combined with the evolutionary information, significantly improves the accuracy of the predicted tertiary structure. From the non-redundant set of protein structures, we derive the 'potential' parameters for the protein secondary structure prediction that contains the structural information of proteins, by following the procedure similar to the way to derive the directional information table of GOR method. Those potential parameters are combined with the frequency matrices obtained by running PSI-BLAST to construct the feature vectors that are used to train the support vector machines (SVM) to build the secondary structure classifiers. Moreover, the problem of huge model file size, which is one of the known shortcomings of SVM, is partially overcome by reducing the size of training data by filtering out the redundancy not only at the protein level but also at the feature vector level. A preliminary result measured by the average three-state prediction accuracy is encouraging.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.149-155
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• 2015

Acyl carrier protein is related with fatty acid biosynthesis in which specific enzymes are involved. Especially, acyl carrier protein (ACP) is the key component in the growing of fatty acid chain. ACP is the small, very acidic protein that covalently binds various intermediates of fatty acyl chain. Acylation of ACP is mediated by holo-acyl carrier protein synthase (ACPS), which transfers the 4'PP-moiety of CoA to the 36th residue Ser of apo ACP. Acyl carrier protein P (ACPP) is one of ACPs from Helicobacter plyori. The NMR structure of ACPP consists of four helices, which were reported previously. Here we show how acylation of ACPP can affect the overall structure of ACPP and figured out the contact surface of ACPP to acyl chain attached during expression of ACPP in E. coli. Based on the chemical shift perturbation data, the acylation of ACCP seems to affect the conformation of the long loop connecting helix I and helix II as well as the second short loop connecting helix II and helix III. The significant chemical shift change of Ile 54 upon acylation supports the contact of acyl chain and the second loop.

• Bulletin of the Korean Chemical Society
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• v.28 no.6
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• pp.1010-1014
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• 2007

M1 RNA is the catalytic component of RNase P, a tRNA-processing enzyme in Escherichia coli. M1 RNA is produced in the cell by transcription of the rnpB gene and subsequent processing at the 3' end. The 3' flanking region of rnpB contains repeated sets of overlapping sequences coding for small proteins. The issue of whether these proteins are expressed remains to be established. In this study, we showed the expression of a small protein encoded by the first repeat within the 3' flanking region of rnpB. Interestingly, protein expression was increased at lower temperatures. The termination efficiency of rnpB terminators was decreased at lower temperatures, suggesting that antitermination is responsible for enhanced protein expression. Moreover, the purified small protein contained M1 RNA, implying a role as a specific RNA-binding protein.

• YAKHAK HOEJI
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• v.44 no.4
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• pp.347-353
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• 2000

To examine influence of artificial digestive juice on the antitumor activity of Ganoderma lucidum-A(GL-A), protein-bound polysaccharide from Ganoderma lucidum, we compared the digested protein-bound polysaccharide with undigested one both on immunopotentiating activity and influence of digestive juices. Protein-bound polysaccharide GL-B was obtained by digesting the antitumor component GL-A with artificial digestive Juices in vitro. When GL-A was administered orally to sarcoma 180 tumor-bearing ICR mice, the life prolonging effect was exhibited in a dose dependent manner Not only GL-A but GL-B increased the production of colony forming unit (CFU) to 10- and 8-fold of that of the control, respectively. Both of the protein-bound polysaccharides also showed the secretion of nitric oxide in RAW 264.7 cell lines to 3.5-and 3.7-fold of that of the control, respectively: GL-A activated components of the alternative complement pathway, whereas GL-B did not. In humoral immunity GL-A increased the activity of alkaline phosphatase in differentiated B cells to 3 times and GL-B to 4 times of that of the control. These results showed that the artificial digestive juices had no influence on the antitumor activity of the protein-bound polysaccharide from Ganoderma lucidum and that its immunomodulating activity retained after treatment with artificial digestive juice. And this provides a basis of the protein-bound polysaccharide of Ganoderma lucidum as an peroral anticancer drug.

• Korean Journal of Animal Reproduction
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• v.16 no.4
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• pp.289-299
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• 1993

The polypeptide patterns of cellular and follicular components were analysed by SDS-PAGE and two dimensional(2-D)electrophoresis combined with isoelectric focusing (IEF) to establish protein profiles in each of the components in porcine follicles. Oocyte-cumulus complexes were cultured in M16+FCS+Gn at 39 in an atmosphere of 5% CO$_2$, in air for 35 h. At the end of the culture, the zona-free oocyte, ZP alone and cumulus cells were prepared and analysed either on 10% SDS-PAGE for the protein profile at the first dimensional gel or 2-D protein pattern. The amounts of each samples were determined for the visualization with Coomasie brilliant blue (CBB) or silver staining, thus giving useful information for the identification of specific proteins in the components or appropriate amount of samples for proper visualization. Oocyte showed 25 and 114 kd major protein band. Other minor components were additionally visualized with CBB on the same gel after silver staining procedure. Cumulus cells also showed specific proteins which is not present in the oocytes. The number of cumulus cell was proper to give major bands with CBB and additional minor bands with silver staining. To establish the degree of contamination from the remnant of the corona radiata to the ZP, zonae were differently prepared or analysed by SDS-PAGE.The preparation of the ZP in this study did not showed any contamination judged by the protein profile of the components. Also follicular fluid showed its specific protein profile without any significant differences among the different sizes of follicles. The established protein profile of each follicular component should be helpful for the identification and elimination of contaminated components, i. e., antigen preparation or immunological studies. The results also suggest that the preparation of each components in the study was appropriate and can be used for a further sensitive biochemical analysis in mammalian oocytes and early embryos.

• Korean Journal of Microbiology
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• v.39 no.3
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• pp.141-147
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• 2003

The simultaneous expression levels of antifungal activity related genes was analyzed by DNA microarray. We constructed DNA chips contained 2,000 randomly digested genome spots of the antifungal bacterium of Bacillus lentimorbus WJ5 and compared its quantitative aspect with 7 antifungal activity deficient mutants induced by gamma radiation ($^{60}Co$). From the analysis of microarray hybridization by the Gene Cluster (Michael Eisen, Stanford Univ.), totally 408 genes were expressed and 20 genes among them were significantly suppressed in mutants. pbuX (xanthine permease, K222), ywbA (phosphotransferase system enzyme II, K393), ptsG (PTS glucose specific enzyme II ABC component, K877), yufO (ABC transporter (ATP-binding protein), K130l), and ftsY (signal recognition particle (docking protein), K868) were simultaneously down-regulated in all mutants. It suggested that they were supposed to be related to the antifungal activity of B. lentimorbus WJ5.

• Korean Journal of Microbiology
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• v.55 no.2
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• pp.112-116
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• 2019

Thp1/PCID2 is a subunit of the evolutionally conserved TREX-2 complex, which is required for transcription-coupled mRNA export from the nucleus to the cytoplasm. In fission yeast, Schizosaccharomyces pombe, there are two orthologs of the Thp1/PCID2 protein. In addition to pci2 (SPBC1105.07c) gene, SPAC1B3.08 gene encodes a PCI domain-containing protein that is predicted as a component of TREX-2 complex. Overexpression of SPAC1B3.08 cause slight defects of both growth and mRNA export. Yeast two-hybrid and co-immunoprecipitation analysis exhibits that the SPAC1B3.08 protein interacted with Sac3 and Dss1, which are another components of TREX-2 complex. These observations support the possibility that the S. pombe SPAC1B3.08 protein, as a component of TREX-2 complex, is involved in mRNA export.

• Molecules and Cells
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• v.47 no.1
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• pp.100001.1-100001.8
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• 2024

In eukaryotes, a primary protein quality control (PQC) process involves the destruction of conformationally misfolded proteins through the ubiquitin-proteasome system. Because approximately one-third of eukaryotic proteomes fold and assemble within the endoplasmic reticulum (ER) before being sent to their destinations, the ER plays a crucial role in PQC. The specific functions and biochemical roles of several E3 ubiquitin ligases involved in ER-associated degradation in mammals, on the other hand, are mainly unknown. We identified 2 E3 ligases, ubiquitin protein ligase E3 component N-recognin 1 (UBR1) and ubiquitin protein ligase E3 component N-recognin 2 (UBR2), which are the key N-recognins in the N-degron pathway and participate in the ER stress response in mammalian cells by modulating their stability. Cells lacking UBR1 and UBR2 are hypersensitive to ER stress-induced apoptosis. Under normal circumstances, these proteins are polyubiquitinated through Lys48-specific linkages and are then degraded by the 26S proteasome. In contrast, when cells are subjected to ER stress, UBR1 and UBR2 exhibit greater stability, potentially as a cellular adaptive response to stressful conditions. Although the precise mechanisms underlying these findings require further investigation, our findings show that cytoplasmic UBR1 and UBR2 have anti-ER stress activities and contribute to global PQC in mammals. These data also reveal an additional level of complexity within the mammalian ER-associated degradation system, implicating potential involvement of the N-degron pathway.

• Journal of Korean Dental Science
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• v.4 no.1
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• pp.6-13
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• 2011

Purpose: Craniosynostosis (CS), one of the most common congenital craniofacial deformities, is the premature closure of cranial sutures. NELL-1 is a novel molecule overexpressed during premature cranial suture closure in human CS. From a functional perspective, NELL-1 has been reported to accelerate chondrocyte maturation and modulate calvarial osteoblast differentiation and apoptosis pathways. The mechanism through which NELL-1 induces these phenomena, however, remains unclear. The purpose of this study is to identify the NELL-1 binding protein(s) through which the biologic mechanism of NELL-1 can be further investigated. Materials and Methods: Far-Western and Immunoprecipitation (IP) assays were performed, independently and in sequence, followed by mass spectrometry to identify the NELL-1 binding proteins. Reverse IP was used to verify and confirm candidate binding protein. Results: The only confirmative protein from current experimentation was vimentin. Vimentin is the major structural component of the intermediate filaments. Conclusion: The present study identified and confirmed vimentin as a NELL-1 binding protein, which opened up a new window to mechanistically facilitate studies on this CS-associated molecule.