• Journal of Microbiology and Biotechnology
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• v.16 no.7
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• pp.1111-1119
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• 2006

Beauvericins and enniatins are cyclohexadepsipeptides exhibiting various biological activities on animal systems, including humans. Fusarium oxysporum FB1501 (KFCC 11363P) that produces four different cyclohexadepsipeptides was isolated from soil in Korea and the structures of the four cyclohexadepsipeptides elucidated by HPLC, MS, IR, and NMR analyses. The molecular weights for compounds 1,2,3, and 4 were determined to be 654.5, 784.5, 668.6, and 682.5, respectively, on the basis of ESI-MS measurements. The IR spectra for all the compounds exhibited absorptions for ester $(1,733-1,743\;cm^{-1})$ and amide $(1,649-1,655\;cm^{-1})$ bonds that were very similar to those for beauvericin and enniatins with ester and amide absorptions. The results of the NMR analysis $(^{1}H,\;^{13}C,\;135-DEPT,\;COSY,\;HMQC,\;and\;HMBC;\;in\;COCl_{3})$ revealed that compounds 1,3, and 4 consisted of $_{L}-N-methyl\;valine$ (N-MeVal), $_{D}-{\alpha}-hydroxyisovaleic\;acid$ (Hiv), and 2-hydroxy-3-methylpentanoic acid (Hmp) residues (compound 1: three N-MeVal residues, two Hiv residues, and one Hmp residue; compound 3: three N-MeVal residues, one Hiv, and two Hmp residues; compound 4: three N-MeVal residues and three Hmp residues). Therefore, the compounds were identified as enniatin H (compound 1), enniatin I (compound 3), and enniatin MK1688 (compound 4). Compound 2 was analyzed as beauvericin according to 1D and 2D NMR analyses. This study is the first report related to the co-production of beauvericin with other unusual enniatins, such as enniatin H, enniatin I, and enniatin MK1688, by Fusarium oxysporum.

• Journal of Microbiology and Biotechnology
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• v.26 no.7
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• pp.1163-1172
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• 2016

The Ω-loop is a nonregular and flexible structure that plays an important role in molecular recognition, protein folding, and thermostability. In the present study, molecular dynamics simulation was carried out to assess the molecular stability and flexibility profile of the porcine trypsin structures. Two Ω-Loops (fragment 57-67 and fragment 78-91) were confirmed to represent the flexible region. Subsequently, glycosylation site-directed mutations (A73S, N84S, and R104S) were introduced within the Ω-loop region and its wing chain based on its potential N-glycosylation sites (Asn-Xaa-Ser/Thr consensus sequences) and structure information to improve the thermostability of trypsin. The result demonstrated that the half-life of the N84S mutant at 50℃ increased by 177.89 min when compared with that of the wild-type enzyme. Furthermore, the significant increase in the thermal stability of the N84S mutant has also been proven by an increase in the T_m values determined by circular dichroism. Additionally, the optimum temperatures of the wild-type enzyme and the N84S mutant were 75℃ and 80℃, respectively. In conclusion, we obtained the thermostability-improved enzyme N84S mutant, and the strategy used to design this mutant based on its structural information and N-linked glycosylation modification could be applied to engineer other enzymes to meet the needs of the biotechnological industry.

• Journal of Integrative Natural Science
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• v.3 no.3
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• pp.143-147
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• 2010

Since it is of great importance to know how a ligand binds to a receptor, there have been a lot of efforts to improve the quality of prediction of docking poses. Earlier efforts were focused on improving search algorithm and scoring function in a docking program resulting in a partial improvement with a lot of variations. Although these are basically very important and essential, more tangible improvements came from the reduction of search space. In a normal docking study, the approximate active site is assumed to be known. After defining active site, scoring functions and search algorithms are used to locate the expected binding pose within this search space. A good search algorithm will sample wisely toward the correct binding pose. By careful study of receptor structure, it was possible to prioritize sub-space in the active site using "receptor-based pharmacophores" or "hot spots". In a sense, these techniques reduce the search space from the beginning. Further improvements were made when the bound ligand structure is available, i.e., the searching could be directed by molecular similarity using ligand information. This could be very helpful to increase the accuracy of binding pose. In addition, if the biological activity data is available, docking program could be improved to the level of being useful in affinity prediction for a series of congeneric ligands. Since the number of co-crystal structures is increasing in protein databank, "Ligand-Guided Docking" to reduce the search space would be more important to improve the accuracy of docking pose prediction and the efficiency of virtual screening. Further improvements in this area would be useful to produce more reliable docking programs.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2209-2213
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• 2007

Ginseng has long been used as a traditional medicine in Asian countries including Korea and China. In recent years, it has been reported that the biological activities of ginseng are due to its active components, ginsenosides. Ginsenosides are represented by triterpenes of the dammarane type. Ginsenoside Re consists of two glucose rings, one rhamnose ring, and the triterpene ring. In the present study ginsenoside Re has been isolated from the Korean ginseng (Panax ginseng) and the tertiary structure has been determined using NMR spectroscopy. Flexibilities around each linkages described by seven torsion angles were considered. The structures of ginsenoside Re obtained by NMR spectroscopy show the rigidity around the glucopyranosyl ring II and alkene side chain. The dihedral angles of φ5, φ6, φ7 are about 150o, 50o and 45o, respectively. In addition, flexibility exists around rhamnopyranosyl and glucopyronosyl moiety. The linkage around the rhamnopyranosyl and glucopyranosyl ring I, are divided into three groups. This flexibility seems to play important role in regulation of the hydrophobic surface exposed to the solvent. Because of the growing need for the structural determination of ginsenoside, this result can help to understand their well-accepted pharmacological effects of ginsenoside Re.

• 한국정보디스플레이학회:학술대회논문집
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• 2008.10a
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• pp.1441-1444
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• 2008

We developed ultra-accelerated quantum chemical molecular dynamics and spectroscopic characterization simulators for development of PDP materials. By combination of these simulators, realistic structure of PDP materials is drawn on the computer. Furthermore, based on the structures, various properties such as cathode luminescence spectrum and secondary electron emission, is successfully evaluated. The strategy of "Experiment integrated Computational Chemistry" using developed simulators will presented that has the potential in being powerful tool for designing the PDP materials.

• BMB Reports
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• v.45 no.5
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• pp.275-280
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• 2012

Nicotinic acetylcholine receptors (nAChRs) are a diverse family of homo- or heteropentameric ligand-gated ion channels. Understanding the physiological role of each nAChR subtype and the key residues responsible for normal and pathological states is important. ${\alpha}$-Conotoxin neuropeptides are highly selective probes capable of discriminating different subtypes of nAChRs. In this study, we performed homology modeling to generate the neuronal ${\alpha}3$, ${\beta}2$ and ${\beta}4$ subunits using the x-ray structure of the ${\alpha}1$ subunit as a template. The structures of the extracellular domains containing ligand binding sites in the ${\alpha}3{\beta}2$ and ${\alpha}3{\beta}4$ nAChR subtypes were constructed using MD simulations and ligand docking processes in their free and ligand-bound states using ${\alpha}$-conotoxin GIC, which exhibited the highest ${\alpha}3{\beta}2$ vs. ${\alpha}3{\beta}4$ discrimination ratio. The results provide a reasonable structural basis for such a discriminatory ability, supporting the idea that the present strategy can be used for future investigations on nAChR-ligand complexes.

• Korean Journal of Veterinary Pathology
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• v.6 no.1
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• pp.41-48
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• 2002

Oval cell is considered as facultative precursor cells for both hepatocytes and biliary cells, as well as origin of hepatocellar and cholangiocellular carcinoma (CCC) during carcinogenesis or toxic liver injury. To clarify the cellular origin or differentiation of cholagiocarcinogensis, the fate of carcinogen-induced oval cells was pathologically and phenotypically chased in Syrian golden hamster liver after Clonorchis sinensis (CS) infection which would give rise to a promoting effect. Two week treatment of hamsters with 0.005% diethylnitrosamine (DEN) followed by 2 week treatment of 1% 2-acetylaminofluorene (AAF) under choline deficient diet resulted in massive proliferation of BrdU labeleed and PCNA positive oval cells showing various distinct morphology, histochemical and immunohistochemical phenotypes for GGT, cytokeratin 19 and OV-6. Oval cells also frequently form ductular-like structures or phenotypically show hepatocyte-like characteristics. After CS infection, the oval cells showed sequential morphological changes to atypicl proliferating bile ductules and all hamsters thereafter developed well differentiated and anaplastic CCC at 16 week after CS infection. In electron microscopy, some bile ductules were constructed by intermediate oval cells and bile ductular cells surrounded by basement membrane. The results of this study strongly suggest that CCC developed in the present study were originated from hepatic stem-like oval cells, supporting the theory of stem cell origin of cancers. In addition, this hamster model would be valuable for the molecular mechanistic study during chemical-triggered cholangiocarcinogenesis.

• Journal of the Korean Vacuum Society
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• v.17 no.5
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• pp.375-380
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• 2008

We have investigated the low-dimensional nanostructures produced by adsorption of triangular Co coplexed dipyrromethane(DPM-trimer, Fig. 1) on graphite surface by using scanning tunneling microscope. DPM-trimer deposition on the graphite surface leads to the formation of long 1-D molecular wires and 2-D hexagonal patterns. We analyzed the heights and structures of 1-D molecular wires and 2-D hexagonal patterns. The 1-D molecular wires were formed 'edge-on' alignments on graphite surface result of continuos $\pi-\pi$ stacking interactions. The other case of 2-D hexagonal patterns were formed 'face-on' alignments on graphite surface.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.14-23
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• 2015

Alzheimer's disease is one of the most common types of degenerative dementia. As a considerable cause of Alzheimer's disease, neurotoxic plaques composed of 39 to 42 residue-long amyloid beta($A{\beta}$) fibrils have been found in the patient's brain in large quantity. A previous study found that erythrosine B (ER), a red color food dye approved by FDA, inhibits the formation of amyloid beta fibril structures. Here, in an attempt to elucidate the inhibition mechanism, we performed molecular dynamics simulations to demonstrate the conformational change of $A{\beta}40$ induced by 2 ERs in atomistic detail. During the simulation, the ERs bound to the surfaces of both N-terminus and C-terminus regions of $A{\beta}40$ rapidly. The observed stacking of the ERs and the aromatic side chains near the N-terminus region suggests a possible inhibition mechanism in which disturbing the inter-chain stacking of PHEs destabilizes beta-sheet enriched in amyloid beta fibrils. The bound ERs block water molecules and thereby help stabilizing alpha helical structure at the main chain of C-terminus and interrupt the formation of the salt-bridge ASP23-LYS28 at the same time. Our findings can help better understanding of the current and upcoming treatment studies for Alzheimer's disease by suggesting inhibition mechanism of ER on the conformational transition of $A{\beta}40$ at the molecular level.

• Fisheries and Aquatic Sciences
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• v.1 no.2
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• pp.227-231
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• 1998

The teleosts represent ancient real-bony vertebrates in phylogeny and resemble major genetic patterns to higher vertebrates. In the present study, we have defined the single family of insulin-like growth factors (IGFs) from flounder (Paralichthys olivaceus), compared to the prototype of IGFs observed in the Agnathan hagfish. In flounder, IGFs are clearly diverged into two major types including type I and II, and they are structurally similar by displaying a multidomain structure consisting of five functional regions as previously found in other vertebrates. However, flIGF-I appears to be more basic (pI 8.03) than the flIGF-II (pI 5.34) in the fully processed form for the B to D domain region. The flIGF-I seems to contain an evolutionary conserved Asn-linked glycosylation in E domain, which is not found in flIGF­II. The most interesting feature is that flIGF-II appeared to be structurally close to hagfish IGF in secondary structures, particularly in Band D domains. This could tell us an idea on the molecular divergence of IGFs from the Agnatha to teleosts during the vertebrate phylogeny. It also support, in part, a notion regarding on how IGF-II is appeared as more embryonic during development. Nonetheless, the biologically active B to D domain region of flIGF-II shows significant sequence homology of $65.6\%$ to flIGF-Is and contains the evolutionary conserved insulin-family signature, as well as a reserved recognition site (Lys) in D domain, necessary to generate proteolytic cleavage for E-peptide. A significant structural difference was found in E domain in which flIGF-I possesses two potential alternative splicing donor site at $Val^{17,\;24}$ of E domain. Therefore, it seems so far that IGF-I sorely produces spliced variants due to the spliced E-peptide moiety while IGF-II appears to be maintained in a single type during evolution. IGF-II, however, may be also possible to transcribe unidentified variants, depending on the physiological conditions of tissues in vertebrates in vivo.