• Journal of the Korea Academia-Industrial cooperation Society
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• v.11 no.3
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• pp.971-977
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• 2010

A flood of biological data has caused many challenges in computing. Bioinformatics, the application of computational techniques to analyze the information associated with biomolecules on a large-scale, has now firmly established itself as an interdisciplinary subject in molecular biology, and encompasses a wide range of subject areas from structural biology, genomics, proteomics, systems biology, biostatistics to computer science. In this review, I provide an introduction and overview of the current state of bioinformatics. Looking at the types of biological information and databases that are commonly used, I also deals with some of bioinformatics application domains which are closely related to areas of computer science.

• BMB Reports
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• v.33 no.1
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• pp.82-88
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• 2000

A homologous gene to alanine racemase was cloned from a hyperthermophilic bacterium, Aquifex pyrophilus. The cloned gene encodes a protein of 341 amino acids, which has a significant homology to alanine racemase of Bacillus stearothermophilus, Lactobacillus brevis, and E. coli. When the gene was expressed in Escherichia coli, it produced a 40 kDa protein. The purified protein contains one mole pyridoxal 5-phosphate per one mole of protein, which is essential for catalytic activity of alanine racemase. The purified protein catalyzed racemization of L-alanine to D-alanine, or vice versa, indicating that the cloned gene encoded alanine racemase. It also showed significant racemization activity against L-serine and ${\alpha}-aminobutylic$ acid. The A. pyrophilus alanine racemase showed strong thermostability, and it maintained catalytic activity in the presence of organic solvents.

• Biodesign
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• v.7 no.1
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• pp.24-27
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• 2019

Pnc1 converts nicotinamide to nicotinic acid to generate NAD⁺ through the Preiss-Handler pathway that is one of the NAD⁺-salvage pathway. By reducing levels of nicotinamide, an inhibitor of the NAD⁺-dependent histone deacetylase Sir2, yeast Pnc1 contributes gene silencing. In this study, to understand the structural features and molecular mechanism of nicotinamidase Pnc1, we overexpressed, purified, and crystallized the N-terminally His₆-tagged Pnc1 protein from Kluyveromyces lactis and obtained X-ray diffraction data at a resolution of 2.2 Å. The crystals of the K. lactis Pnc1 (KlPnc1) belonged to space group P2₁2₁2₁ with unit cell parameters a=38.5, b=77.3, c=83.3, and α=β=γ= 90°. There is one molecule in the asymmetric unit.

• Anatomy and Cell Biology
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• v.56 no.1
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• pp.9-15
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• 2023

An accessory submandibular gland is a rare variation. As such, there is limited literature regarding the embryology, anatomy, variations, clinical imaging, and pathology of the accessory submandibular gland. In this article, we review the existing literature on the accessory submandibular gland from clinical and anatomical perspectives. The goal of this review is to provide comprehensive knowledge of this variation which can be useful for oral and maxillofacial/head and neck surgeons, radiologists, and anatomists. Within this review, the embryologic origin as well as the anatomy of the accessory submandibular gland is detailed. Several imaging modalities which can be used to visualize the accessory submandibular gland are outlined as well as its variations. Lastly, this review investigates several reported clinical considerations regarding the accessory submandibular gland including sialoliths, Wharton's duct obstruction, and pleomorphic adenoma.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3297-3300
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• 2010

In this study, the 3D-QSARs (three-dimensional quantitative structure-activity relationships: CoMFA and CoMSIA) between structural changes of N-phenyl-O-phenylthionocarbamate analogues (1-30) and their fungicidal activities against the capsicum phytophthora (Phyophthora capsici) fungi were analyzed, then considered quantitatively in terms of minimum structural requirements for fungicidal evaluation. The statistical qualities ($r^2_{cv.}$ = 0.510 and $r^2_{ncv.}$ = 0.948) of the optimal CoMFA 1 model are improved over the other models in the conditions of field combinations, and the two alignments. In the optimal CoMFA 1 model, relative contribution percentages of the CoMFA field were: steric field, 52.3%; electrostatic field, 37.8%; hydrophobic field, 9.9%. Results were similar for the CoMFA 2 model. Therefore, the steric field of the analogues had the highest contribution ratio for fungicidal activity. Specifically, with the contour map of steric fields, the fungicidal activity increased when bulky steric Y-substituents were introduced to the meta-position on the N-phenyl ring and small steric Y-subsituents were introduced to its para-position.

• Journal of the Korean Magnetic Resonance Society
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• v.8 no.1
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• pp.1-18
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• 2004

A thioredoxin from hyperthermophile, Methanococcus jannashii (MjTRX) was characterized by use of the differential scanning calorimetry to understand the mechanisms of thermodynamic stability. MjTRX has an unfolding transition temperature of 116.5$^{\circ}C$, although the maximum free energy of the unfolding (9.9 Kcal/mol) is similar to that of E. coli thioredoxin (ETRX, 9.0 Kcal/mol). However, the temperature of maximum stability is higher than ETRX by 20$^{\circ}C$, indicating that the unfolding transition temperature increased by shifting the temperature of maximum stability. MjTRX has lower enthalpy and entropy of the unfolding compared to ETRX maintaining a similar free energy of the unfolding. From the structure and the thermodynamic parameters of MjTRX, we showed that the unfolding transition temperature of MjTRX is increased due to the decreased entropy of the unfolding. Decreasing the unfolded state entropy and increasing the folded state entropy can decrease the entropy of the unfolding. In the case of MjTRX, the increased number of proline residues decreased the unfolded state entropy and the increased enthalpy in the folded state increased the folded state entropy.

• Journal of the Korean Magnetic Resonance Society
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• v.28 no.1
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• pp.1-5
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• 2024

IscU, the iron-sulfur (Fe-S) cluster scaffold protein, is an essential protein for biogenesis of Fe-S clusters. Previous studies showed that IscU manifests a metamorphic structural feature; at least two structural states, namely the structured state (S-state) and the disordered state (D-state), interconverting in a physiological condition, was observed. Moreover, subsequent studies demonstrated that the metamorphic flexibility of IscU is important for its Fe-S cluster assembly activity as well as for an efficient interaction with various partner proteins. Although solution nuclear magnetic resonance (NMR) spectroscopy has been a useful tool to investigate this protein, the detailed molecular mechanism that sustains the structural heterogeneity of IscU is still unclear. To tackle this issue, we applied a high-pressure NMR (HP-NMR) technique to the IscU variant, IscU(I8K), which shows an increased population of the S-state. We found that the equilibrium between the S- and D-state was significantly perturbed by pressure application, and the specific regions of IscU exhibited more sensitivity to pressure than the other regions. Our results provide novel insights to appreciate the dynamic behaviors of IscU and the related versatile functionality.

• Journal of Industrial Technology
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• v.24 no.B
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• pp.139-142
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• 2004

To identify conserved structural or functional subunit(s) in the CP1 (editing) domains of class Ia tRNA synthetases, five available structures were compared and analyzed. Through sequence alignments of the CP1 domains, three conserved regions were found near the amino acid binding site in the editing domain. Structural overlapping of the three subunits clearly showed that there exist three common structural subunits in all of the five editing RS structures. The new alignment suggests a translocation movement of the CP1 domain caused by the binding with tRNA. Based on the experimental and modeling results, it is proposed that subunits 1 and 3 accommodate the incoming amino acid binding, while subunit 2 contributes to the interactions with the adenosine ring of the A76 to stabilize the overall tRNA binding.. Since these subunits are critical for the editing reaction, we expect that these key structures should be conserved through all class Ia editing RSs.

• Proceedings of the Korean Biophysical Society Conference
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• 2002.06b
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• pp.50-50
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• 2002

The heterologous expression of sodN gene from Streptomyces seoulensis in Streptomyces lividans together with the gel filtration and sedimentation equilibrim data indicated that the quaternary structure of NiSOD is homohexamer, which is novel among SODs, not the previously reported homotetramer. The EPR spectrum of $^{61}$ Ni (I = 3/2) substituted NiSOD showed a clear resolved hyperfine structure at g=2.016, unambiguously identifying that the EPR signal from NiSOD is due to Ni.(omitted)

• BMB Reports
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• v.49 no.3
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• pp.159-166
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• 2016

Several members of tumor necrosis factor receptor (TNFR) superfamily that these members activate caspase-8 from death-inducing signaling complex (DISC) in TNF ligand-receptor signal transduction have been identified. In the extrinsic pathway, apoptotic signal transduction is induced in death domain (DD) superfamily; it consists of a hexahelical bundle that contains 80 amino acids. The DD superfamily includes about 100 members that belong to four subfamilies: death domain (DD), caspase recruitment domain (CARD), pyrin domain (PYD), and death effector domain (DED). This superfamily contains key building blocks: with these blocks, multimeric complexes are formed through homotypic interactions. Furthermore, each DD-binding event occurs exclusively. The DD superfamily regulates the balance between death and survival of cells. In this study, the structures, functions, and unique features of DD superfamily members are compared with their complexes. By elucidating structural insights of DD superfamily members, we investigate the interaction mechanisms of DD domains; these domains are involved in TNF ligand-receptor signaling. These DD superfamily members play a pivotal role in the development of more specific treatments of cancer.