• The Korean Journal of Pesticide Science
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• 제10권3호
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• pp.157-164
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• 2006

Three dimensional quantitative structure-activity relationships (3D-QSARs) for the fungicidal activities against Rhizoctonia solani (RS) and Phytophthora capsici (PC) by N-phenyl substituents(X) of N-phenylthionocarbamate derivatives were studied quantitatively using comparative molecular field analysis (CoMFA) methodology based on different alignment approaches. Statistical quality of CoMFA models with field fit alignment were slightly higher than that of atom based fit alignment. The optimized CoMFA models (RS: RF2 & PC: PF2) were derived from field fit alignment and combination of CoMFA fields. And the statistical results of the two models showed the best predictability of the fungicidal activities based on the cross-validated value $q^2$ ($r^2_{cv.}$ =RS: 0.557 & PC: 0.676) and non-cross-validated value ($r^2_{ncv.}$ =RS: 0.954 & PC: 0.968), respectively. The selective fungicidal activities between two fungi were dependence upon the electrostatic field of substrate molecule. Therefore, the fungicidal activities from CoMFA contour maps showed that the fungicidal activity will be able to increased according to the modification of X-substituents on the substrate molecules.

• Journal of KIISE:Databases
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• 제31권6호
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• pp.641-649
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• 2004

The relationship between chemical structures and biological activities is researched briskly in the area of 'Medicinal Chemistry' At the base of these structure-based drug design tries, medicinal chemists search the existing drugs of similar chemical structure to target drug for the development of a new drug. Therefore, it is such necessary that an automatic system selects drug files that have a set of chemical moieties matching a user-defined query moiety. Substructure searching is the process of identifying a set of chemical moieties that match a specific query moiety. Testing for substructure searching was developed in the late 1950s. In graph theoretical terms, this problem corresponds to determining which graphs in a set are subgraph isomorphic to a specified query moiety. Testing for subgraph isomorphism has been proved, in the general case, to be an NP- complete problem. For the purpose of overcoming this difficulty, there were computational approaches. On the 1990s, a US patent has been granted on an atom-centered indexing scheme, used by the RS3 system; this has the virtue that the indexes generated can be searched by direct text comparison. This system is commercially used(http://www.acelrys.com/rs3). We define the RS3 system's drawback and present a new indexing scheme. The RS3 system treats substructure searching with substring matching by means of expressing chemical structure aspredefined strings. However, it has insufficient 'rerall' and 'precision‘ because it is impossible to index structures uniquely for same atom and same bond. To resolve this problem, we make the minimum-cost- spanning tree for one centered atom and describe a structure with paths per levels. Expressing 2D chemical structure into 1D a string has limit. Therefore, we break 2D chemical structure into 1D structure fragments. We present in this paper a new index technique to improve recall and precision surprisingly.

• Proceedings of the Ginseng society Conference
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• 고려인삼학회 1998년도 Advances in Ginseng Research - Proceedings of the 7th International Symposium on Ginseng -
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• pp.115-126
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• 1998

Four new dammarnae-glycosides named ginsenosides Rgs, Rh4, RsB and Rf2 have been isolated 1'rom Korean red ginseng, the root of Panax ginseng C. A. Meyer (Araliaceae) and their chemical structures have been elucidated by chemical and spectroscopic methods, including'H-'H COSY, HMQC, HMBC, NOESY, as 3-0- [$\beta$-D-glucopyranosyl(1 ~2)-$\beta$-D-glucopyranosyl] dammar-20(22) , B4-diene-3P,12P-diol (ginsenoside Rgs),6-0-$\beta$-D-glucopyranosyl-dammar-20(22),24-diene-3P,6P, 12P-triol (ginsenoside Rh4),3-0- [6" -0-acetyl-D-glucopyranosyl(1 ~2)--D-glucopyranosyl] 20(5)- protopanaxadiol (ginsenoside Rs3) and 6-0- [u-L-rhamno-pyranosyl(1 ~2)-$\beta$-D-glucopyranosyl] dammarane -3$\beta$, 6a, 12 $\beta$, 20(R),25-pentol(ginsenoslde Rfa). The absolute stereo structure of a double bond at C-20(22) was determined as entgegen type by applying NOESY.OESY.

• Genomics & Informatics
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• 제19권3호
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• pp.29.1-29.10
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• 2021

In our previous studies, we have demonstrated the association of certain variants of the thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), and thyroglobulin (TG) genes with congenital hypothyroidism. Herein, we explored the mechanistic basis for this association using different in silico tools. The mRNA 3'-untranslated region (3'-UTR) plays key roles in gene expression at the post-transcriptional level. In TSHR variants (rs2268477, rs7144481, and rs17630128), the binding affinity of microRNAs (miRs) (hsa-miR-154-5p, hsa-miR-376a-2-5p, hsa-miR-3935, hsa-miR-4280, and hsa-miR-6858-3p) to the 3'-UTR is disrupted, affecting post-transcriptional gene regulation. TPO and TG are the two key proteins necessary for the biosynthesis of thyroid hormones in the presence of iodide and H₂O₂. Reduced stability of these proteins leads to aberrant biosynthesis of thyroid hormones. Compared to the wild-type TPO protein, the p.S398T variant was found to exhibit less stability and significant rearrangements of intra-atomic bonds affecting the stoichiometry and substrate binding (binding energies, ΔG of wild-type vs. mutant: -15 vs. -13.8 kcal/mol; and dissociation constant, K_d of wild-type vs. mutant: 7.2E^-12 vs. 7.0E^-11 M). The missense mutations p.G653D and p.R1999W on the TG protein showed altered ΔG(0.24 kcal/mol and 0.79 kcal/mol, respectively). In conclusion, an in silico analysis of TSHR genetic variants in the 3'-UTR showed that they alter the binding affinities of different miRs. The TPO protein structure and mutant protein complex (p.S398T) are less stable, with potentially deleterious effects. A structural and energy analysis showed that TG mutations (p.G653D and p.R1999W) reduce the stability of the TG protein and affect its structure-functional relationship.

• The Journal of Korean Obstetrics and Gynecology
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• 제18권4호
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• pp.10-23
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• 2005

Purpose : This study is to examine the ability of Rhizoma Scirpi (RS) to induce HeLa cell viability. Methods : We culture HeLa cell which is human metrocarcinoma cell in D-MEM included 10% fetal bovine serum(Hyclone Laboratories) below $37^{\circ}C$, 5% CO2. Then we observed apoptosis of log phage cell which is changed cultivation liquid 24 Hours periodically. Results : 1. RS induces mitochondria membrane potential collapse. 2. P38 MAPK is involved in RS-induced death in HeLa cells. 3. P38 MAPK is involved in RS-induced apoptosis in HeLa cells. 4. P38 MAPK reguates RS-induced caspase-3, -8 and -9 activation in HeLa cells. 5. The inhibition of caspase regulates RS-induced cell death in HeLa cells. 6. RS induces mitochondria membrane potential collapse in HeLa cells. 7. P38 MPK is involved in the regulation of Bcl-2 and Bfu in HeLa cells.8. RS regulates the expression of Bcl-2 and Bax in HeLa cells. 9. SR induces p38 MAPK activation in HeLa cells. Conclusion : RS induces apoptosis in HeLa cells via p38 MAPK activation.

• Korean Journal of Microbiology
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• 제47권1호
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• pp.14-21
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• 2011

Riboflavin synthase catalyzes the formation of one molecule of each riboflavin and 5-amino-6-ribitylamino-2,4-pyrimidinedione by the transfer of a 4-carbon moiety between two molecules of the substrates, 6,7-dimetyl-8-ribityllumazine. The most remarkable feature is the sequence similarity between the N-terminal half (1-97) and the C-terminal half domain (99-213). To investigate the structure and fluorescent characteristics of the N-terminal half of riboflavin synthase (N-RS) in Escherichia coli, more than 10 mutant genes coding for the mutated N-terminal domain of riboflavin synthase were generated by polymerase chain reaction. The genes coding for the proteins were inserted into pQE vector designed for easy purification of protein by 6X-His tagging system, expressed, and the proteins were purified. Almost all mutated N-terminal domain of riboflavin synthases bind to 6,7-dimethyl-8-ribityllumazine and riboflavin as fluorescent ligands. However, N-RS C47D and N-RS ET66,67DQ mutant proteins show colorless, indicating that fluorescent ligands were dissociated during purification. In addition, most mutated proteins show low fluorescent intensity comparing to N-RS wild type, whereas N-RS C48S posses stronger fluorescent intensity than that of wild type protein. Based on this result, N-RS C48S can be used as the tool for high throughput screening system for searching for the compound with inhibitory effect for the riboflavin synthase.

• Journal of Korea Society of Industrial Information Systems
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• 제9권2호
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• pp.17-22
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• 2004

In this paper, a concatenated RS and Turbo code is proposed for OFDM system over burst error channel. The concatenated code used in this study is a RS(255,202) code and a rate 1/2 turbo code. The turbo code uses 2 recursive systematic convolutional (RSC) code as the constituent codes and the parity bit are punctured to get the desired code rate. It is shown by simulation that the conventional OFDM system fails when there exists burst noise. The concatenated RS and turbo code obtains at least 5dB gain over the turbo code at the bit error probability of 10/sup -3/.

• Biomedical Science Letters
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• 제13권2호
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• pp.105-110
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• 2007

Aspartyl-tRNA synthetase (AspRS) exists in two different forms with respect to tRNA recognition. The discriminating enzyme (D-AspRS) recognizes only tRNA$^{Asp}$, while the non-discriminating one (ND-AspRS) also recognizes tRNA$^{Asn}$ and therefore forms both Asp-tRNA$^{Asn}$ and Asp-tRNA$^{Asp}$. Plus primary sequence distinguishes two general groups of AspRS. There is a predominantly bacterial-type, larger AspRS (about 580 aa) in addition to a shorter archaeal/eukaryotic type (about 430 aa). In vivo data made clear that discriminating and non-discriminating enzymes exist in both groups. The determinants in the protein sequence responsible for tRNA discrimination are not hewn. The AspRS from Acidithiobacillus ferrooxidans might be suggested ND-AspRS fur missing of AsnRS in genomic sequencing data. Therefore, we analyzed the AspRS from A. ferrooxidans with in vitro aminoacylation assay with E. coli unfractionated tRNA, in vivo missense suppression assay with tipA34 mutant and Northern hybridization with probes which were specific with tRNA$^{Asp}$ or tRNA$^{Asn}$. The AspRS from A. ferrooxidans produced more Asp-tRNA than that from E. coli. Only aspS gene from A. ferrooxidans suppressed trpA34 strain in minimal media without tryptophan. Only AspRS from A. ferrooxidans showed mischarged Asp-tRNA$^{Asn}$ band. Therefore, AspRS from A. ferrooxidans is definitely ND-AspRS.

• Archives of Pharmacal Research
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• 제20권3호
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• pp.280-282
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• 1997

A genuine dammarane-glycoside, named as ginsenoside $ Rs_3$, was isolated from the MeOH extracts of Korean red ginseng (Panax ginseng C.A. Meyer) through repeated silica gel column chromatographies and its chemical structure was determined as (20S)-protopanaxadiol $3-O-[6^{11}-O-acetyl-{\beta}-D-glucopyranosyl (1{\rightarrow2)-{\beta}-D-$glucopyranoside on the basis of several spectral and physical evidences including HMBC and FAB-MS.

• Journal of the Korean Electrochemical Society
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• 제2권2호
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• pp.98-105
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• 1999

In the present study, buoyant force and its stabilizing effects in an electrostatic field were examined systematically in order to reduce the effect of natural convection with thermal stratification in a horizontal fluid-saturated porous layer. The correlation of ionic mass transport induced by double-diffusive convection in a horizontal porous layer has been derived theoretically. And the theoretical model was examined by electrochemical experiments. The theoretical correlation for mass transport which is satisfying Forchheimer's flow equation and based on the micro-turbulence model is derived as a function of soltual Darcy-Rayleigh number, thermal Darcy-Rayleigh number and Lewis number. In the experiment, the mass transport of copper ions in $CuSO_4-H_2SO_4$ solution is measured by electrochemical technique. By assembling theoretical correlation and experimental results, the mass transport correlation induced by double-diffusive convection is proposed as $$Sh=\frac{0.03054(Rs_D-LeRa_D)^{1/2}}{1-3.8788(Rs_D-LeRa_D)^{-1/10}}$$ The present correlation looks flirty reasonable with comparing experimental results, and very promising for the applications of its prototype into various systems involving heat transfer as well as mass transfer, in order to control the effects of natural convection effectively.