• Journal of Microbiology and Biotechnology
• /
• v.12 no.6
• /
• pp.890-894
• /
• 2002

A xylanase-producing Trichoderma strain was isolated from soil. Xylanase from Trichoderma strain SY was purified 21-fold to an apparent homogeneity, with a $17.4\%$ yield. The optimum pH and temperature were determined to be 5.5 and $50^{\circ}C$, respectively, and its molecular weight was 21-kDa by SDS-PAGE. The corresponding gene, named xyl, was cloned by RT-PCR. DNA blot analysis of xyl showed that this gene is present as a single copy. The amino acid sequence of the Xyl protein showed similarity to those of other xylanases derived from various fungi. mRNA of xyl was highly expressed when this fungus was grown on cellulose or xylan as a sole carbon source, but undetectable when grown on sucrose. Extracts of Escherichia coli cells expressing xyl were found to have xylanase activity. It was confirmed that xyl from this isolate encodes xylanase.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.2
• /
• pp.455-458
• /
• 2011

In previous report, with the aid of receptor-oriented pharmacophore-based in silico screening, we characterized three novel hPNMT inhibitors (YPN010, YPN016, and YPN017) and proposed that the hydrogen bonding interaction between inhibitors and side chain of Lys57 is very important to inhibitory activity of hPNMT. To confirm the importance of Lys57, mutant with substitution of Lys57 with Ala was cloned and binding study was performed for a K57A mutant of hPNMT using STD-NMR and fluorescence experiments. The binding constants for three novel inhibitors with mutant hPNMT were dramatically decreased compared to those with wild-type protein. K57A mutant-induced conversion of noradrenaline to adrenaline was suppressed about 95 % compared to wild-type hPNMT. Mutagenic analysis using a K57A mutant confirmed the importance of the Lys57 residue in binding of the inhibitor candidate to hPNMT as well as enzymatic activity of hPNMT, implying that these results are consistent with our binding model.

• Bulletin of the Korean Chemical Society
• /
• v.28 no.3
• /
• pp.379-385
• /
• 2007

Receptor-oriented pharmacophore-based in silico screening is a powerful tool for rapidly screening large number of compounds for interactions with a given protein. Inhibition of the enzyme catechol-Omethyltransferase (COMT) offers a novel possibility for treating Parkinson's disease. Bisubstrate inhibitors of COMT containing the adenine of S-adenosylmethionine (SAM) and a catechol moiety are a new class of potent and selective inhibitor. In the present study, we used receptor-oriented pharmacophore-based in silico screening to examine the interactions between the active site of human COMT and bisubstrate inhibitors. We generated 20 pharmacophore maps, of which 4 maps reproduced the docking model of hCOMT and a bisubstrate inhibitor. Only one of these four, pharmacophore map I, effectively described the common features of a series of bisubstrate inhibitors. Pharmacophore map I consisted of one hydrogen bond acceptor (to Mg2+), three hydrogen bond donors (to Glu199, Glu90, and Gln120), and one hydrophobic feature (an active site region surrounded by several aromatic and hydrophobic residues). This map represented the most essential pharmacophore for explaining interactions between hCOMT and a bisubstrate inhibitor. These results revealed a pharmacophore that should help in the development of new drugs for treating Parkinson's disease.

• Journal of Applied Biological Chemistry
• /
• v.55 no.1
• /
• pp.67-70
• /
• 2012

Plant MYB transcription factors regulate secondary metabolism, cellular morphogenesis, and plant hormone signaling pathway. MYB proteins in plants consist of two repeats of 50 amino acid residues, which are referred to as R2R3 and they interact with WD40 or basic helix loop helix (bHLH) proteins. Yeast two hybrid assay was determined whether rice MYB protein interacts with either OsTTG1, which contains a WD40 domain, or with OsGL3, which contains a bHLH domain. Among 30 OsMYB proteins, three interacted with OsTTG1 and five interacted with OsGL3. A series of MYB mutants were created to determine the MYB domain important for the interaction with OsTTG1 or OsGL3. By using the yeast two hybrid assay, we found that the R3 motif of OsMYB10 and the R2 motif of OsMYB16 were required for interaction with OsTTG1 and OsGL3 proteins, respectively.

• Bulletin of the Korean Chemical Society
• /
• v.26 no.8
• /
• pp.1225-1228
• /
• 2005

C-terminal fragments of APP (APP-CTs), that contain A$\beta$ sequence, are found in neurotic plaques, neurofibrillary tangles and the cytosol of lymphoblastoid cells obtained from AD patients. CT26, Thr639-Asp664 (TVIVITLVMLKKKQYTSIHH GVVEVD) includes not only the transmembrane domain but also the cytoplasmic domain of APP. This sequence is produced from cleavage of APP by caspase and $\gamma$-secretase. In this study, the solution structure of CT26 was investigated using NMR spectroscopy and circular dichroism (CD) spectropolarimeter in various membrane-mimicking environments. According to CD spectra and the tertiary structure of CT26 determined in TFE-containing aqueous solution, CT26 has an α-helical structure from $Val^{2}\;to\;Lys^{11}$ in TFE-containing aqueous solution. However, according to CD data, CT26 adopts a $\beta$-sheet structure in the SDS micelles and DPC micelles. This result implies that CT26 may have a conformational transition between $\alpha$-helix and $\beta$-sheet structure. This study may provide an insight into the conformational basis of the pathological activity of the C-terminal fragments of APP in the model membrane.

• Journal of Ginseng Research
• /
• v.35 no.4
• /
• pp.471-478
• /
• 2011

Ginseng, the root of Panax ginseng, is one of the oldest herbal medicines. It has a variety of physiological and pharmacological effects. Recently, we isolated a subset of glycolipoproteins that we designated gintonin, and demonstrated that it induced transient change in intracellular calcium concentration $([Ca^{2+}]_i)$ in cells via G-protein-coupled receptor signaling pathway(s). The previous method for gintonin isolation included multiple steps using methanol, butanol, and other organic solvents. In the present study, we developed a much simple method for the preparation of gintonin from ginseng root using 80% ethanol extraction. The extracted fraction was designated edible gintonin. This method produced a high yield of gintonin (0.20%). The chemical characteristics of gintonin such as molecular weight and the composition of the extract product were almost identical as the gintonin prepared using the previous extraction regimen involving various organic solvents. We also examined the physiological effects of edible gintonin on endogenous $Ca^{2+}$-activated $Cl^-$ channel activity of Xenopus oocytes. The 50% effective dose was $1.03{\pm}0.3\;{\mu}g$/mL. Finally, since gintonin preparation through ethanol extraction is easily reproducible, gintonin could be commercially applied for ginseng-derived functional health food and/or drug following the confirmations of in vitro and in vivo physiological and pharmacological effects of gintonin.

• Genomics & Informatics
• /
• v.6 no.4
• /
• pp.166-172
• /
• 2008

A multitude of protein-coding sequence variations (CVs) in the human genome have been revealed as a result of major initiatives, including the Human Variome Project, the 1000 Genomes Project, and the International Cancer Genome Consortium. This naturally has led to debate over how to accurately assess the functional consequences of CVs, because predicting the functional effects of CVs and their relevance to disease phenotypes is becoming increasingly important. This article surveys and compares variation databases and in silico prediction programs that assess the effects of CVs on protein function. We also introduce a combinatorial approach that uses machine learning algorithms to improve prediction performance.

• Genomics & Informatics
• /
• v.16 no.1
• /
• pp.2-9
• /
• 2018

Olfactory receptors (ORs) in mammals are generally considered to function as chemosensors in the olfactory organs of animals. They are membrane proteins that traverse the cytoplasmic membrane seven times and work generally by coupling to heterotrimeric G protein. The OR is a G protein-coupled receptor that binds the guanine nucleotide-binding $G{\alpha}_{olf}$ subunit and the $G{\beta}{\gamma}$ dimer to recognize a wide spectrum of organic compounds in accordance with its cognate ligand. Mammalian ORs were originally identified from the olfactory epithelium of rat. However, it has been recently reported that the expression of ORs is not limited to the olfactory organ. In recent decades, they have been found to be expressed in diverse organs or tissues and even tumors in mammals. In this review, the expression and expected function of olfactory receptors that exist throughout an organism's system are discussed.

• Genomics & Informatics
• /
• v.14 no.1
• /
• pp.2-11
• /
• 2016

The advances in mass spectrometry-based proteomics technologies have enabled the generation of global proteome data from tissue or body fluid samples collected from a broad spectrum of human diseases. Comparative proteomic analysis of global proteome data identifies and prioritizes the proteins showing altered abundances, called differentially expressed proteins (DEPs), in disease samples, compared to control samples. Protein biomarker candidates that can serve as indicators of disease states are then selected as key molecules among these proteins. Recently, it has been addressed that cellular pathways can provide better indications of disease states than individual molecules and also network analysis of the DEPs enables effective identification of cellular pathways altered in disease conditions and key molecules representing the altered cellular pathways. Accordingly, a number of network-based approaches to identify disease-related pathways and representative molecules of such pathways have been developed. In this review, we summarize analytical platforms for network-based protein biomarker discovery and key components in the platforms.

• Genomics & Informatics
• /
• v.6 no.1
• /
• pp.50-53
• /
• 2008

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.