• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• BMB Reports
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• 제41권2호
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• pp.102-107
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• 2008

Extracellular proteases play an important role in a wide range of host physiological events, such as food digestion, extracellular matrix degradation, coagulation and immunity. Among the large extracellular protease family, serine proteases that contain a "paper clip"-like domain and are therefore referred to as CLIP-domain serine protease (clip-SP), have been found to be involved in unique biological processes, such as immunity and development. Despite the increasing amount of biochemical information available regarding the structure and function of clip-SPs, their in vivo physiological significance is not well known due to a lack of genetic studies. Recently, Drosophila has been shown to be a powerful genetic model system for the dissection of biological functions of the clip-SPs at the organism level. Here, the current knowledge regarding Drosophila clip-SPs has been summarized and future research directions to evaluate the role that clip-SPs play in Drosophila immunity are discussed.

• BMB Reports
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• 제42권3호
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• pp.166-171
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• 2009

Hsp70s assist in the process of protein folding through nucleotide-controlled cycles of substrate binding and release by alternating from an ATP-bound state in which the affinity for substrate is low to an ADP-bound state in which the affinity for substrate is high. It has been long recognized that the two-domain structure of Hsp70 is critical for these regulated interactions. Therefore, it is important to obtain information about conformational changes in the relative positions of Hsp70 domains caused by nucleotide binding. In this study, analytical ultracentrifugation and dynamic light scattering were used to evaluate the effect of ADP and ATP binding on the conformation of the human stress-induced Hsp70.1 protein. The results of these experiments showed that ATP had a larger effect on the conformation of Hsp70 than ADP. In agreement with previous biochemical experiments, our results suggest that conformational changes caused by nucleotide binding are a consequence of the movement in position of both nucleotide- and substrate-binding domains.

• 한국환경농학회지
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• 제39권1호
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• pp.26-35
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• 2020

BACKGROUND: Microbes that govern a unique biochemical process of oxidizing ammonia into dinitrogen gas, such as anaerobic ammonium oxidation (anammox) have been reported to play a pivotal role in agricultural soils and in oceanic environments. However, limited information for anammox bacterial abundance and distribution in the terrestrial habitats has been known. METHODS AND RESULTS: Phylogenetic and next-generation sequencing analyses of bacterial 16S rRNA gene were performed to examine potential anammox bacteria in paddy soils. Through clone libraries constructed by using the anammox bacteria-specific primers, some clones showed sequence similarities with Planctomycetes (87% to 99%) and anammox bacteria (94% to 95%). Microbial community analysis for the paddy soils by using Illumina Miseq sequencing of 16S rRNA gene at phylum level was dominated by unclassified Bacteria at 33.2 ± 7.6%, followed by Chloroflexi at 20.4 ± 2.0% and Acidobacteria at 17.0 ± 6.5%. Planctomycetes that anammox bacteria are belonged to was 1.5% (± 0.3) on average from the two paddy soils. CONCLUSION: We suggest evidence of anammox bacteria in the paddy soil. In addition to the relatively well-known microbial processes for nitrogen-cycle, anammox can be a potential contributor on the cycle in terrestrial environments such as paddy soils.

• Natural Product Sciences
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• 제17권3호
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• pp.189-197
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• 2011

To examine the bone-protective effects of Puerariae Radix (PR) in an estrogen-deficient animal model, we treated ovariectomized rats with PR at a dose of 10.0 mg/kg 3 times a week for 16 weeks. Our results showed that PR increased mineral content and density of the trabecular bone at the neck of the left femur. Moreover, biochemical data indicated that PR had a positive effect on bone turnover. No endometrial hyperplasia was detected in the PR group. The present data suggest that PR should be considered for use in the treatment of bone loss in women with postmenopausal osteoporosis.

• 한국물환경학회지
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• 제31권3호
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• pp.313-318
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• 2015

To study the influence of changes in river discharge on water quality of the main stem of the Geum River, we investigated variation of inflow load from tributaries with river discharge. We also studied the mixing behavior of pollutants during mixing of waters of the main stem and Gap Stream. For this study, we collected water quality data such as suspended solids (SS), biochemical oxygen demand (BOD), chemical oxygen demand (COD), total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) representing pre-monsoon, monsoon, and post-monsoon events of 2013 from a website of Water Information System. Based on inflow load, the Gap and Miho streams may be ones of tributaries which may largely influence water quality of main stem in upper river region. The Suksung and Nonsan Streams seemed to further affect water quality downstream. Results of modified EMMA indicated SS and TP may have another source(besides Gap Stream) at pre-monsoon, monsoon, and post-monsoon period. In contrast, TN and organic matter (BOD, COD, TOC) were conservative at pre-monsoon and post-monsoon. However, when river discharge increased, these pollutants may also came from unspecified non-point sources. Therefore, we need to attempt to find non-point sources for the pollutants in the main channel of upper Geum River region.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.38-38
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• 2011

Covalently bonded halogen ligands possess unusual charge distributions, attracting both electrophilic and nucleophilic molecular ligands to form halogen bonds. In many biochemical systems, halogen bonds and hydrogen bonds coexist. The interplay between halogen and hydrogen bonds has been actively studied in various three-dimensional bulk molecular co-crystals. It was found that halogen bonds could be complementary to hydrogen bonds due to their similar bond strength and dissimilar directionality. In those ensemble-averaging approaches, however, it was not possible to extract local information such as individual bond configurations and nano-level domain structures, which is a crucial part of supramolecular studies. In this study, we directly visualize the individual molecular configuration of a brominated molecule and the role of halogen bonds on Au(111) using scanning tunneling microscopy. The precise arrangement of observed molecular structures was reproduced by first-principle studies and explained in the context of halogen and hydrogen bonds. We discuss the distances and the strengths of the observed halogen bonds and hydrogen bonds, which are consistent with previous bulk data.

• 한국어업기술학회:학술대회논문집
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• 한국어업기술학회 2000년도 춘계수산관련학회 공동학술대회발표요지집
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• pp.381-381
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• 2000

Lectin binding assay was conducted on 3 A. tamarense isolates (AT-A, AT-2 and AT-6). Fatty acid composition of all 3 isolates was analyzed, and total carotenoid content and $\beta$-carotene were also determined. AT-A and AT-2 treated with different lectins in this study showed the positive response, whereas potentially toxic AT-6 did not bind DBA lectin, regardless of different growth phase, but conjugated ConA, PNA, RCA, SBA, UEA and WGA. It is possible that DBA is a desirable method for rapid and easy discrimination of highly toxic A. tamarense. AT-A, AT-2 and AT-6 comprised saturated fatty acids (49.0-61.9%), monounsaturated fatty acids (8.0-20.5%) and polyunsaturated fatty acids (23.2-30.5%). In particular, 22:6 (n-3) polyunsaturated fatty acid in AT-6 had a high abundance, compared with AT-A and AT-2. However, carotenoid content and $\beta$-carotene were not contributed to discriminate each isolate. Due to variability in biochemical composition at different isolates, possibly DBA and 22:6 (n-3) polyunsaturate fatty acid provide a good information for discrimination of AT-6.

• 한국수정란이식학회지
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• 제11권1호
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• pp.71-80
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• 1996

The envelope of the rnannnalian oocyte plays crucial roles in sperm-oocyte interactions by providing sperm receptors, inducing acrosome reaction and preventing polyspermy. Understanding of properties of the zona pellucida (ZP) is essential for the artificial control of fertility in mammals. This study was carried out to produce and characterize monoclonal antibodies(MAbs) to porcine ZP proteins. Approximately 8,000 ZPs were obtained from follicular oocytes and dissolved in 40$\mu$l of double distilled water. Following immunization through foot-pad injections of Balb /c mice with a ZP solution, the popliteal lymph nodes were recovered at 2 weeks after the last injection. Hybridoma cell lines were established by fusing lymph node cells with P3X63 myeloma cells through selection using HAT medium and screening by immunofluorescence(IF) microscopy on the isolated ZP. Secreted MAbs were found to consist k chains and different heavy chains as evidenced by isotyping. Some of the MAbs demonstrated high specificity to the ZP in IF. The Mabs also showed positive cross reactivity with hamster and mouse eggs, while negative with bovine eggs. The results implicate that the MAbs can be used not only for identification of functional regions of the ZP, but also for elucidation of mechanisms involved in fertilization of mammals. The MAbs will provide basic information on biochemical anatomy of the ZP as well as can be candidates for the future contraceptive vaccines.

• Journal of Species Research
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• 제5권2호
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• pp.235-240
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• 2016

To investigate the indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined taxonomically. The isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. As an outcome of this study, 10 unrecorded bacterial species belonging to the phylum Firmicutes were discovered from various sources such as soil, tidal flat, fresh water, sea water, kimchi and gut of Fulvia mutica. The unrecorded species were assigned to 7 different genera of 5 families, namely Bacillus and Ornithinibacillus of Bacillaceae, Exiguobacterium of Exiguobacteriaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Staphylococcus of Staphylococcaceae, and Lactococcus of Streptococcaceae. The selected isolates were subjected to further taxonomic characterization including the analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. The descriptive information on the 10 unrecorded species are provided.