• Genomics & Informatics
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• v.13 no.2
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• pp.45-52
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• 2015

Acute myeloid leukemia is a well characterized blood cancer in which the unnatural growth of immature white blood cell takes place, where several genes transcription is regulated by the micro RNAs (miRNAs). Argonaute (AGO) protein is a protein family that binds to the miRNAs and mRNA complex where a strong binding affinity is crucial for its RNA silencing function. By understanding pattern recognition between the miRNAs-mRNA complex and its binding affinity with AGO protein, one can decipher the regulation of a particular gene and develop suitable siRNA for the same in disease condition. In the current work, HOXA9 gene has been selected from literature, whose deregulation is well-established in acute myeloid leukemia. Four miRNAs (mir-145, mir-126, let-7a, and mir-196b) have been selected to target mRNA of HOXA9 (NCBI accession No. NM_152739.3). The binding interaction between mRNAs and mRNA of HOXA9 gene was studied computationally. From result, it was observed mir-145 has highest affinity for HOXA9 gene. Furthermore, the interaction between miRNAs-mRNA duplex of all chosen miRNAs are docked with AGO protein (PDB ID: 3F73, chain A) to study their interaction at molecular level through an in silico approach. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding of AGO-assisted miRNA based gene silencing mechanism in HOXA9 gene associated in acute myeloid leukemia computationally.

• Proceedings of the Korea Information Processing Society Conference
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• 2007.11a
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• pp.452-455
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• 2007

생명과학 기술의 급속한 발달로 인류 복지 증진에 많은 기여를 하였지만 아직도 각종 질병 등으로 많은 사람들이 고통 받고 있으며, 이를 극복하기 위한 연구 및 기술개발은 세계 각처에서 계속되고 있다. 이러한 연구 및 기술개발의 결과로 산출되는 생명정보 데이터의 양은 기하급수적으로 증가하고 있기에 이런 방대한 양의 생명정보 데이터를 분석하고 분석된 데이터에서 인류 복지에 유용한 정보를 얻기 위한 생명정보학(Bioinformatics)이 등장하게 되었다. 이에, 한국과학기술정보연구원(KISTI)은 IT 기반 생명정보 인프라 구축의 중심기관으로 CCBB(Center for Conputationa Biology & Bioinformatics) 웹사이트를 운영하고 있다. CCBB는 전산학적인 기술을 이용한 생명현상 연구를 지원하기 위하여 21종의 생명정보 콘텐트(DB 및 분석도구)를 수집 분석 구축 제공하고 있다. 이 중에서 GenBank, PDB, PIR, Swiss-prot 등의 데이터베이스는 KISTI에서 개발한 KRISTAL 검색엔진을 통하여 국내에서도 빠르고 쉽게 검색 가능하도록 자체 구축하고 있으며, 이와 더불어 BLAST, FASTA, ClustalW 등의 주요 분석 도구 또한 제공하고 있다. 본 논문에서는 CCBB에서 제공중인 21종의 콘텐트 중에서 GenBank, REBASE, GeneCards, InterProScan 등 4종의 대용량 고효율 생명정보 콘텐트의 소개 및 업데이트 방법에 관한 내용을 기술하고자 한다.

• Biomolecules & Therapeutics
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• v.32 no.3
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• pp.390-398
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• 2024

FoxO1, a member of the Forkhead transcription factor family subgroup O (FoxO), is expressed in a range of cell types and is crucial for various pathophysiological processes, such as apoptosis and inflammation. While FoxO1's roles in multiple diseases have been recognized, the target has remained largely unexplored due to the absence of cost-effective and efficient inhibitors. Therefore, there is a need for natural FoxO1 inhibitors with minimal adverse effects. In this study, docking, MMGBSA, and ADMET analyses were performed to identify natural compounds that exhibit strong binding affinity to FoxO1. The top candidates were then subjected to molecular dynamics (MD) simulations. A natural product library was screened for interaction with FoxO1 (PDB ID-3CO6) using the Glide module of the Schrödinger suite. In silico ADMET profiling was conducted using SwissADME and pkCSM web servers. Binding free energies of the selected compounds were assessed with the Prime-MMGBSA module, while the dynamics of the top hits were analyzed using the Desmond module of the Schrödinger suite. Several natural products demonstrated high docking scores with FoxO1, indicating their potential as FoxO1 inhibitors. Specifically, the docking scores of neochlorogenic acid and fraxin were both below -6.0. These compounds also exhibit favorable drug-like properties, and a 25 ns MD study revealed a stable interaction between fraxin and FoxO1. Our findings highlight the potential of various natural products, particularly fraxin, as effective FoxO1 inhibitors with strong binding affinity, dynamic stability, and suitable ADMET profiles.

• Journal of the Mineralogical Society of Korea
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• v.17 no.1
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• pp.61-73
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• 2004

The purposes of this study are to investigate the occurrence, the hydrochemical characteristics and the origin of the $CO_2$-rich springs from the Kangwon Province, and to reanalyze the previous studied results of other researchers. The $CO_2$-rich water samples were collected at 13 locations in the Kangwon Province. The $CO_2$-rich water shows a high $CO_2$ concentration ($P_{CO2}$ 0.787 to 4.78 atm), weak acidic pHs, electrical conductivity values ranging from 422 to 2,280 $\mu$S/cm, and high Fe and F contents. The chemical compositions of $CO_2$-rich water from this study area are classified into three types; $Ca-HCO_3$, Ca(Na)-$HCO_3$, $Na-HCO_3$ types. The chemical data of $CO_2$-rich waters and their host rocks indicate that $Na-HCO_3$ type water are mainly influenced by biotite, K-feldspar granite, and Ca(Na)-HC $O_3$, type water is chiefly influenced by gneiss and carbonate minerals in granite. F and Fe contents of $CO_2$-rich waters are abundant in $Na-HCO_3$, and $Ca-HCO_3$ types, respectively. The results of this study suggest that the chemical composition $CO_2$-rich water is mainly controlled by the mineralogical composition of aquifer host rocks. Oxygen and deuterium isotope data indicate that $CO_2$-rich water is meteoric origin. The $\delta^{13}$C values (-0.3$\textperthousand$ to -6.2$\textperthousand$ PDB) suggest that dissolved carbonates are mainly derived from a deep-seated $CO_2$ and partly from carbonate minerals.

• The Korean Journal of Mycology
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• v.35 no.1
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• pp.47-53
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• 2007

In this study, we investigated the properties of incubation and growing of Pleurotus eryngii in addition to the mycological properties to use them as basic data for breeding. The speed of mycelial growth on the MCM was faster than on the PDA. The biomass in the PDB broth culture was higher than in the MCM and YMG broth culture. KNR2515 and KNR2516 required 19 days for growth of mycelia on commercial sawdust media. KNR2503 required 6.5 days and 15.3 days for pin-heading and harvesting, respectively. In morphological properties by the mushroom, the heights of KNR2312 and KNR2322 were 122.7 and 121.0 mm, respectively. The thickness of KNR2322 and KNR2513 were 39.8 mm and 31.3 mm, respectively. The weight of KNR2524's fruiting body was 36.3 g, which is good as wild strain. The quality of fruiting body of KNR2503 was 4.0 in comparison to the score 7 of commercially cultivated strains. KNR2512 had the darkest color of pileus with L value 43.6. The slow growing strains, KNR2511, KNR2513, and KNR2512 had the bright pileus with L value 80. In morphological characteristics, KNR2511, KNR2513, and KNR2515 had white lamellar and plane pileus. The three strains are supposed to be the same group and KNR2516 and KNR2518 appeared to be related to the group. The commercially cultivated strains had convex pileus, KNR2502, KNR2503, KNR2504, KNR2521, and KNR2525 had infundibuliform, and the other strains had plane pileus. Several strains were valuable for breeding, JNR2503 for growth rate, KNR2512 for pileus color, and KNR2312, KNR2322, KNR2503, and KNR2513 for the quality.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.18 no.1
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• pp.40-46
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• 2013

The isotope ratios of $^{13}C/^{12}C$ and $^{18}O/^{16}O$ for a sample in a mass spectrometer are measured relative to those of a pure $CO_2$ reference gas (i.e., laboratory working standard). Thus, the calibration of a laboratory working standard gas to the international isotope scales (Pee Dee Belemnite (PDB) for ${\delta}^{13}C$ and Vienna Standard Mean Ocean Water (V-SMOW) for ${\delta}^{18}O$) is essential for comparisons between data sets obtained by other groups on other mass spectrometers. However, one often finds difficulties in getting well-calibrated standard gases, because of their production time and high price. Additional difficulty is that fractionation processes can occur inside the gas cylinder most likely due to pressure drop in long-term use. Therefore, studies on laboratory production of pure $CO_2$ isotope standard gas from stable solid calcium carbonate standard materials, have been performed. For this study, we propose a method to extract pure $CO_2$ gas without isotope fractionation from a solid calcium carbonate material. The method is similar to that suggested by Coplen et al., (1983), but is better optimized particularly to make a large amount of pure $CO_2$ gas from calcium carbonate material. The $CaCO_3$ releases $CO_2$ in reaction with 100% pure phosphoric acid at $25^{\circ}C$ in a custom designed, evacuated reaction vessel. Here we introduce optimal procedure, reaction conditions, and samples/reactants size for calcium carbonate-phosphoric acid reaction and also provide the details for extracting, purifying and collecting $CO_2$ gas out of the reaction vessel. The measurements for ${\delta}^{18}O$ and ${\delta}^{13}C$ of $CO_2$ were performed at Seoul National University using a stable isotope ratio mass spectrometer (VG Isotech, SIRA Series II) operated in dual-inlet mode. The entire analysis precisions for ${\delta}^{18}O$ and ${\delta}^{13}C$ were evaluated based on the standard deviations of multiple measurements on 15 separate samples of purified $CO_2$. The pure $CO_2$ samples were taken from 100-mg aliquots of a solid calcium carbonate (Solenhofen-ori $CaCO_3$) during 8-day experimental period. The multiple measurements yielded the $1{\sigma}$ precisions of ${\pm}0.01$‰ for ${\delta}^{13}C$ and ${\pm}0.05$‰ for ${\delta}^{18}O$, comparable to the internal instrumental precisions of SIRA. Therefore, we conclude the method proposed in this study can serve as a way to produce an accurate secondary and/or laboratory $CO_2$ standard gas. We hope this study helps resolve difficulties in placing a laboratory working standard onto the international isotope scales and does make accurate comparisons with other data sets from other groups.

• Journal of Mushroom
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• v.6 no.1
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• pp.32-37
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• 2008

This study was carried out to investigate the growth inhibition of Propionibacterium acnes by mycelial culture broth of Paecilomyces japonica in the Mulberry leaf extract. The growth inhibition effect of P. japonica mycelial culture broth against P. acnes in various concentration of Mulberry leaf extract was the most effective in 3% Mulberry leaf extract. The inhibition effect of P. japonica mycelial culture broth against P. acnes according to the culture time was the moust effective after 25 days mycelial cultivation. As the treating amount of the mycelial culture broth was increased, the growth inhibition effect against P. acnes was increased gradually. The growth inhibition effect of mycelial culture broth against P. acnes according to the time of heat treatment was active by 45min at $100^{\circ}C$, while it was inactive more than 60min at $100^{\circ}C$. This result suggested that the antibacterial materials are possible to be glycoside or peptides. Taken together P. japonica mycelial culture in the Mulbarry leaf extract has a possibility to be an element of skin-care cosmetics regulating the acnes.

• Journal of Microbiology and Biotechnology
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• v.27 no.12
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• pp.2119-2128
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• 2017

Citrinin (CIT) is a toxic secondary metabolite produced by fungi belonging to the Penicillium, Aspergillus, and Monascus spp. This toxin has been detected in many agricultural products. In this study, a strain Y3 with the ability to eliminate CIT was screened and identified as Cryptococcus podzolicus, based on the sequence analysis of the internal transcribed spacer region. Neither uptake of CIT by cells nor adsorption by cell wall was involved in CIT elimination by Cryptococcus podzolicus Y3. The extracellular metabolites of Cryptococcus podzolicus Y3 stimulated by CIT or not showed no degradation for CIT. It indicated that CIT elimination was attributed to the degradation of intracellular enzyme(s). The degradation of CIT by C. podzolicus Y3 was dependent on the type of media, yeast concentration, temperature, pH, and initial concentration of CIT. Most of the CIT was degraded by C. podzolicus Y3 in NYDB medium at 42 h but not in PDB medium. The degradation rate of CIT was the highest (94%) when the concentration of C. podzolicus Y3 was $1{\times}10^8cells/ml$. The quantity of CIT degradation was highest at $28^{\circ}C$, and there was no degradation observed at 3$5^{\circ}C$. The study also showed that acidic condition (pH 4.0) was the most favorable for CIT degradation by C. podzolicus Y3. The degradation rate of CIT increased to 98% as the concentration of CIT was increased to $20{\mu}g/ml$. The toxicity of CIT degradation product(s) toward HEK293 was much lower than that of CIT.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• Journal of Microbiology and Biotechnology
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• v.26 no.10
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• pp.1708-1716
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• 2016

Glucose dehydrogenase (GDH) is an oxidoreductase enzyme and is used as a biocatalyst to regenerate NAD(P)H in reductase-mediated chiral synthesis reactions. In this study, the glucose 1-dehydrogenase B gene (gdhB) was cloned from Bacillus thuringiensis subsp. kurstaki, and wild-type (GDH-BT^WT) and His-tagged (GDH-BT^N-His, GDH-BT^C-His) enzymes were produced in Escherichia coli BL21 (DE3). All enzymes were produced in the soluble forms from E. coli. GDH-BT^WT and GDH-BT^N-His showed high specific enzymatic activities of 6.6 U/mg and 5.5 U/mg, respectively, whereas GDH-BT^C-His showed a very low specific enzymatic activity of 0.020 U/mg. These results suggest that the intact C-terminal carboxyl group is important for GDH-BT activity. GDH-BT^WT was stable up to 65℃, whereas GDH-BT^N-His and GDH-BT^C-His were stable up to 45℃. Gel permeation chromatography showed that GDH-BT^WT is a dimer, whereas GDH-BT^N-His and GDH-BT^C-His are monomeric. These results suggest that the intact N- and C-termini are required for GDH-BT to maintain thermostability and to form its dimer structure. The homology model of the GDH-BT^WT single subunit was constructed based on the crystal structure of Bacillus megaterium GDH (PDB ID 3AY6), showing that GDH-BT^WT has a Rossmann fold structure with its N- and C-termini located on the subunit surface, which suggests that His-tagging affected the native dimer structure. GDH-BT^WT and GDH-BT^N-His regenerated NADPH in a yeast reductase-mediated chiral synthesis reaction, suggesting that these enzymes can be used as catalysts in fine-chemical and pharmaceutical industries.