• Bulletin of the Korean Chemical Society
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• 제31권1호
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• pp.52-58
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• 2010

Human histamine H1 receptor (HHR1) is a G protein-coupled receptor and a primary target for antiallergic therapy. Here, the ligand-based three-dimensional pharmacophore models were built from a set of known HHR1 inverse agonists using HypoGen module of CATALYST software. All ten generated pharmacophore models consist of five essential features: hydrogen bond acceptor, ring aromatic, positive ionizable and two hydrophobic functions. Best model had a correlation coefficient of 0.854 for training set compounds and it was validated with an external test set with a high correlation value of 0.925. Using this model Maybridge database containing 60,000 compounds was screened for potential leads. A rigorous screening for drug-like compounds unveiled RH01692 and SPB00834, two novel molecules for HHR1 with good CATALYST fit and estimated activity values. The new lead molecules were docked into the active site of constructed HHR1 homology model based on recently crystallized squid rhodopsin as template. Both the hit compounds were found to have critical interactions with Glu177, Phe432 and other important amino acids. The interpretations of this study may effectively be deployed in designing of novel HHR1 inverse agonists.

• Interdisciplinary Bio Central
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• 제1권1호
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• pp.3.1-3.6
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• 2009

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

• 한국미생물·생명공학회지
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• 제46권3호
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• pp.234-243
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• 2018

남극해에는 산업적으로 유용한 신규 효소촉매를 생산하는 미생물들이 들어 있다. 우리는 로스해(Ross Sea)로부터 분리한 여러 저온성 박테리아를 조사하였으며, 그 중에서 지방분해 능력이 뛰어난 Croceibacter atlanticus (No. 40-F12)를 찾았다. Shotgun 클로닝 방법으로 리파아제 유전자(lipCA)를 찾았으며 Escherichia coli 균에서 LipCA 효소를 발현하였다. Spain Arreo metagenome alpha/beta hydrolase를 기준으로 LipCA 상동구조모델을 만들어서 분석한 결과, ${\alpha}/{\beta}$ hydrolase fold, Gly-X-Ser-X-Gly motif, 그리고 lid 구조를 갖고 있기 때문에 전형적인 리파아제 효소임이 밝혀졌다. Ammonium sulfate 침전법과 겔여과 크로마토그래피를 통해서 세포추출액으로부터 LipCA 효소를 순수하게 분리한 후, 최적 온도, pH, 안정성, 기질특이성, 유기용매 안정성 등의 효소특성을 규명하였다. LipCA를 cross-linked enzyme aggregate (CLEA) 방법으로 고정화하고 효소특성을 조사, 비교하였다. 고정화를 통해 온도, pH, 유기용매에 대한 안정성이 증가하였고 기질특이성의 변화는 관찰되지 않았다. $LipCA^{CLEA}$는 원심분리 방법으로 쉽게 회수되었고 4번의 재사용 후에 40% 이상의 활성이 잔재하였다. 이 논문은 C. atlanticus 리파아제의 발현, 특성규명, Cross-linked Enzyme Aggregated 고정화를 바탕으로 안정성을 높여 산업적 활용 가능성을 제시한 최초의 보고이다.

• BMB Reports
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• 제40권6호
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• pp.861-869
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• 2007

The enzyme 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR; EC1.1.1.34) catalyzes the first committed step of isoprenoids biosynthesis in MVA pathway. Here we report for the first time the cloning and characterization of a full-length cDNA encoding HMGR (designated as CgHMGR, GenBank accession number EF206343) from hazel (Corylus avellana L. Gasaway), a taxol-producing plant species. The full-length cDNA of CgHMGR was 2064 bp containing a 1704-bp ORF encoding 567 amino acids. Bioinformatic analyses revealed that the deduced CgHMGR had extensive homology with other plant HMGRs and contained two transmembrane domains and a catalytic domain. The predicted 3-D model of CgHMGR had a typical spatial structure of HMGRs. Southern blot analysis indicated that CgHMGR belonged to a small gene family. Expression analysis revealed that CgHMGR expressed high in roots, and low in leaves and stems, and the expression of CgHMGR could be up-regulated by methyl jasmonate (MeJA). The functional color assay in Escherichia coli showed that CgHMGR could accelerate the biosynthesis of $\beta$-carotene, indicating that CgHMGR encoded a functional protein. The cloning, characterization and functional analysis of CgHMGR gene will enable us to further understand the role of CgHMGR involved in taxol biosynthetic pathway in C. avellana at molecular level.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.135-135
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• 2017

The Gramene database (http://www.gramene.org) is a powerful online resource for agricultural researchers, plant breeders and educators that provides easy access to reference data, visualizations and analytical tools for conducting cross-species comparisons. Learn the benefits of using Gramene to enrich your lectures, accelerate your research goals, and respond to your organismal community needs. Gramene's genomes portal hosts browsers for 44 complete reference genomes, including crops and model organisms, each displaying functional annotations, gene-trees with orthologous and paralogous gene classification, and whole-genome alignments. SNP and structural diversity data, available for 11 species, are displayed in the context of gene annotation, protein domains and functional consequences on transcript structure (e.g., missense variant). Browsers from multiple species can be viewed simultaneously with links to community-driven organismal databases. Thus, while hosting the underlying data for comparative studies, the portal also provides unified access to diverse plant community resources, and the ability for communities to upload and display private data sets in multiple standard formats. Our BioMart data mining interface enable complex queries and bulk download of sequence, annotation, homology and variation data. Gramene's pathway portal, the Plant Reactome, hosts over 240 pathways curated in rice and inferred in 66 additional plant species by orthology projection. Users may compare pathways across species, query and visualize curated expression data from EMBL-EBI's Expression Atlas in the context of pathways, analyze genome-scale expression data, and conduct pathway enrichment analysis. Our integrated search database and modern user interface leverage these diverse annotations to facilitate finding genes through selecting auto-suggested filters with interactive views of the results.

• Clinical and Experimental Reproductive Medicine
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• 제26권2호
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• pp.225-230
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• 1999

In mouse, the heat shock protein 70-2 (hsp70-2) is found to have special function in spermatogenesis. Based on the observation, the hypothesis that human hspA2 (human gene; 98.2% amino acid homology with hsp70-2) might have important function in spermatogenesis in human testes was proposed. To test the hypothesis, we examined the expression of hspA2 in human tissues. Expression vector pDMC4 for expression of the human hspA2 protein using pTricHisB (invitrogen, USA) was constructed and the expressed hspA2 protein was cross-reacted with antiserum 2A raised against mouse hsp70-2 protein. Based on the cross-reactivity, we determined the expression level of hspA2 protein in human tissues by western blot analysis using the antiserum 2A. We demonstrated that antiserum 2A antibodies detected human hspA2 protein with specificity which was produced in the E.coli expression system. On Western blot analyses, significant hspA2 expression was observed in testes with normal spermatogenesis, whereas a low level of hspA2 was expressed in testis with Sertoli-cell only syndrome. Also, a small amount of hspA2 was detected in breast, stomach, prostate, colon, liver, ovary, and epididymis. These results demonstrate that the hspA2 protein is highly expressed in male specific germ cells, which in turn suggests that hspA2 protein might playa specific role during meiosis in human testes as suggested in the murine model. However, further studies should be attempted to determine the function of hspA2 protein in human spermatogenesis.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제31권3호
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• pp.219-227
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• 2005

Purpose: Abnormalities in the p53 gene are regarded as the most consistent genetic abnormalities detected in head and neck squamous cell carcinogenesis. Two new members of the p53 gene family, p73 and p63 have recently been identified. They share considerable sequence homology with p53 in the transactivation, DNA binding, and oligomerization domains, indicating possible involvement in carcinogenesis. Disruption of the homeostatic balance between proliferation and apoptosis is widely believed to contribute to human oral carcinogenesis. The aim of this study was to analyze expression of p63 in squamous cell carcinogenesis and to compare with immunochemical markers representing cell proliferation and apoptosis. Materials and Methods: Using the Syrian hamster oral cancer model, the fraction of apoptotic (apoptotic index-AI), proliferating (mitotic index-MI) and p63 expressing keratinocytes were examined at normal, dysplastic and malignant oral epithelium using the TUNEL assay, PCNA and p63 immunostaining. Results: p63 significantly increased between normal and dysplastic epithelium and between dysplastic and malignant epithelium. PCNA significantly increased between normal and dysplastic epithelium and between normal and malignant epithelium. However, increase between dysplastic and malignant epithelium, though still increasing, was not statistically significant. The percentage of TUNEL positive cells increased from normal to dysplastic epithelium and returned to normal keratinocyte level in the malignant epithelium. However, differences between tissue types were not significant. The ratio of MI:AI increased significantly only in the dysplastic-malignant epithelial transition. The increase of p63 expression closely reflected the change in the MI:AI ratio during oral carcinogenesis. Conclusion: The p63 may be associated with the regulation of epithelial proliferation and apoptosis in DMBA-induced hamster buccal pouch squamous cell carcinogenesis. Further study is required to investigate which p63 isoforms are involved in hamster buccal pouch carcinogenesis.

• Molecules and Cells
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• 제38권8호
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• pp.685-696
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• 2015

Rice is a model plant widely used for basic and applied research programs. Plant cell wall proteins play key roles in a broad range of biological processes. However, presently, knowledge on the rice cell wall proteome is rudimentary in nature. In the present study, the tightly-bound cell wall proteome of rice callus cultured cells using sequential extraction protocols was developed using mass spectrometry and bioinformatics methods, leading to the identification of 1568 candidate proteins. Based on bioinformatics analyses, 389 classical rice cell wall proteins, possessing a signal peptide, and 334 putative non-classical cell wall proteins, lacking a signal peptide, were identified. By combining previously established rice cell wall protein databases with current data for the classical rice cell wall proteins, a comprehensive rice cell wall proteome, comprised of 496 proteins, was constructed. A comparative analysis of the rice and Arabidopsis cell wall proteomes revealed a high level of homology, suggesting a predominant conservation between monocot and eudicot cell wall proteins. This study importantly increased information on cell wall proteins, which serves for future functional analyses of these identified rice cell wall proteins.

• 생태와환경
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• 제52권3호
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• pp.221-230
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• 2019

섬진강 수계에 서식하는 누치(Hemibarbus labeo)의 미토콘드리아 DNA에서 cytochrome c oxidase subunit I(COI) 유전자를 발굴하고 누치속 Hemibarbus 및 잉어과(Cyprinidae) 내 계통유전학적인 위치를 확인하는 연구를 수행하였다. 발굴된 577 bp COI 시컨스의 다중배열 결과 섬진강산 누치들의 높은 염기서열 상동성을 보였다(99~100%). 우리나라에서 발견되는 누치속 3종에서 누치(H. labeo: HD1)와 어름치(H. mylodon)의 염기서열 유사성은 88.91%, 참마자 (H. longirostis)와는 88.81%이었다. 또한, H. maculatus, H. meditus, H. umbrifer, H. barbus는 각각 누치와의 염기서열 유사성이 98.97%, 97.20%, 96.87%, 98.85% 등으로 나타났다. 누치속 7종의 계통유전학적 분석결과 섬진강산 누치(H. labeo)들은 두개의 단계통 (clade)을 형성하는데 하나는 하동, 임실, 강진, 순창의 섬진강 누치들로만 이루어진 단계통, 다른 하나는 하동의 HD2, HD8, HD9와 국내 부산, 아산, 서울 등에서 채집 보고된 누치들과 단계통을 형성하였다. 잉어과 내 섬진강산누치(HD1)의 계통진화적 위치는 피라미(Zacco platypus)와는 진화적 거리가 0.143, 누치속 H. maculatus와는 0.006으로 나타났다. 또한 잉어과 28종 내 계통유전학적 위치는 모래무지아과(Gobioninae) 어류들이 포함된 그룹 I에 섬진강산 누치가 위치함을 확인하였다. 본 연구의 결과는 누치를 포함하는 잉어과 내 어류의 계통유전학적 비교와 환경오염에 따른 담수환경 모니터링을 위한 모델어류의 발굴연구에 주요한 유전적 정보를 제공할 것이다.

• Journal of Ginseng Research
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• 제43권3호
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• pp.460-474
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• 2019

Background: Ginsenoside compound K (CK) is a promising drug candidate for rheumatoid arthritis. This study examined the impact of polymorphisms in NR1I2, adenosine triphosphate-binding cassette (ABC) transporter genes on the pharmacokinetics of CK in healthy Chinese individuals. Methods: Forty-two targeted variants in seven genes were genotyped in 54 participants using Sequenom MassARRAY system to investigate their association with major pharmacokinetic parameters of CK and its metabolite 20(S)-protopanaxadiol (PPD). Subsequently, molecular docking was simulated using the AutoDock Vina program. Results: ABCC4 rs1751034 TT and rs1189437 TT were associated with increased exposure of CK and decreased exposure of 20(S)-PPD, whereas CFTR rs4148688 heterozygous carriers had the lowest maximum concentration ($C_{max}$) of CK. The area under the curve from zero to the time of the last quantifiable concentration ($AUC_{last}$) of CK was decreased in NR1I2 rs1464602 and rs2472682 homozygous carriers, while $C_{max}$ was significantly reduced only in rs2472682. ABCC4 rs1151471 and CFTR rs2283054 influenced the pharmacokinetics of 20(S)-PPD. In addition, several variations in ABCC2, ABCC4, CFTR, and NR1I2 had minor effects on the pharmacokinetics of CK. Quality of the best homology model of multidrug resistance protein 4 (MRP4) was assessed, and the ligand interaction plot showed the mode of interaction of CK with different MRP4 residues. Conlusion: ABCC4 rs1751034 and rs1189437 affected the pharmacokinetics of both CK and 20(S)-PPD. NR1I2 rs1464602 and rs2472682 were only associated with the pharmacokinetics of CK. Thus, these hereditary variances could partly explain the interindividual differences in the pharmacokinetics of CK.