• 한국자기공명학회논문지
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• 제16권2호
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• pp.162-171
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• 2012

SAV2228 has an OB (Oligomer-Binding)-motif which is frequently used for nucleic acid recognition. To characterize the activity of translation initiation factor-1 (IF-1) from Staphylococcus aureus, SAV2228 was expressed and purified in Escherichia coli. We acquired 3D NMR spectra showing well dispersed and homogeneous signals which allow us to assign 94.4% of all $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$ and $^{13}CO$ resonances. We could predict a secondary structure of SAV2228 using TALOS and CSI from NMR data. SAV2228 was consisted of one ${\alpha}$-helix and five ${\beta}$-sheets. The predicted secondary structure, ${\beta}-{\beta}-{\beta}-{\alpha}-{\beta}-{\beta}$, was similar to other bacterial IF-1, but it was not completely same to the eukaryotic one. Assigned NMR peaks and secondary structre prediction can be used for the study on interaction with nucleic acid in the future.

• 국제초고층학회논문집
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• 제5권4호
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• pp.263-270
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• 2016

In this paper, the stability requirements for diagrid and mega braced structures are examined. The role of the secondary bracing system for the stability of a diagrid structure is discussed. A simple procedure is proposed for the design of the secondary bracing system when it is required. As a case study, the design of the Hearst Tower diagrid and its secondary bracing system are presented.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.268-274
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• 2003

Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even far small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins.

• 사물인터넷융복합논문지
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• 제7권4호
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• pp.15-21
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• 2021

본 연구에서는 농촌지역에 목구조로 형성된 건축유산의 소방안전대책이 갖는 문제점 파악하고, 개선책을 제시하고자 한다. 문제점 도출을 위하여 연구대상으로 당진지역에 현존하는 목구조로 형성된 천주교 공소의 건물 구조, 주변 환경 등 문화유산의 특수성을 파악하고, 천주교 공소에서 발생 가능한 화재와 안전 요소에 대하여 분석하였다. 그 결과 목구조 공소가 갖는 역사성과 장소성, 지역의 정체성을 갖는 중요한 문화유산 임에도, 화재 등 안전에 대한 취약성 및 소방 활동을 위한 화재 인지 및 초기 화재 대응에 어려움 등 방재시스템의 문제가 나타났다. 따라서 좀 더 강화된 방화 등에 방재 체제가 필요하며, 목구조 공소의 특성에 적합한 소방 시설을 설치하고 방화활동에 주체를 확보하여 건축유산인 공소의 방재체계를 개선해야 할 필요성이 도출되었으며, 또한 공소는 대부분 농촌지역에 위치하고 있어 산불과 같은 자연재난에서 목구조 공소 방재 활동을 강화하고 화재 시 대응방안과 마련이 시급한 것으로 나타났다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.287-293
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• 2005

Predicting RNA secondary structure as accurately as possible is very important in functional analysis of RNA molecules. However, different prediction methods and related parameters including terminal GU pair of helices, minimum length of helices, and free energy systems often give different prediction results for the same RNA sequence. Then, which structure is more important than the others? i.e. which combinations of the methods and related parameters are the optimal? In order to investigate above problems, first, three prediction methods, namely, random stacking of helical regions (RS), helical regions distribution (HD), and Zuker's minimum free energy algorithm (ZMFE) were compared by taking 1139 tRNA sequences from Rfam database as the samples with different combinations of parameters. The optimal parameters are derived. Second, Zuker's dynamic programming method for prediction of RNA secondary structure was revised using the above optimal parameters and related software BJRNAFold was developed. Third, the effects of short-range interaction were studied. The results indicated that the prediction accuracy would be improved much if proper short-range factor were introduced. But the optimal short-range factor was difficult to determine. A user-adjustable parameter for short-range factor was introduced in BJRNAFold software.

• 한국자기공명학회논문지
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• 제11권2호
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• pp.73-84
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• 2007

MTH1821 (UniProtKB/TrEMBL ID O27849) is a 96-residue hypothetical protein from the open reading frame of Methanobacterium thermoautotrophicum H one of the target organisms of structural genomics pilot project. Proteins which contain conserved sequence compared with MTH1821 have not been discovered yet and the functional and structural information for MTH1821 is not available. Here, we present the sequence-specific backbone resonance using multidimensional heteronuc1ear NMR spectroscopy and propose the secondary structure using GetSBY software. The backbone resonances of N, HN, $C_{\alpha}$, $C_{\beta}$, CO and $H_{\alpha}$ which are necessary for a prediction of secondary structure by GetSBY were assigned about 98% (557/568). The secondary structure of MTH1821 confirmed that it is comprised of four strand regions and two helical regions. This report will provide a valuable resource for the calculation solution structure of MTH1821 and for the other hypothetical protein that is targeted for structural-based functional discovery.

• BMB Reports
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• 제47권10호
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• pp.558-562
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• 2014

OASL1 is a member of the 2'-5'-oligoadenylate synthetase (OAS) family and promotes viral clearance by activating RNase L. OASL1 interacts with the 5'-untranslated region (UTR) of interferon regulatory factor 7 (Irf7) and inhibits its translation. To identify the secondary structure required for OASL1 binding, we examined the 5'-UTR of the Irf7 transcript using "selective 2'-hydroxyl acylation analyzed by primer extension" (SHAPE). SHAPE takes advantage of the selective acylation of residues in single-stranded regions by 1-methyl-7-nitroisatoic anhydride (1M7). We found five major acylation sites located in, or next to, predicted single-stranded regions of the Irf7 5'-UTR. These results demonstrate the involvement of the stem structure of the Irf7 5'-UTR in the regulation of Irf7 translation, mediated by OASL1.

• 한국지진공학회논문집
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• 제24권4호
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• pp.179-187
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• 2020

Seismic qualification of equipment including piping is performed by using floor response spectra (FRS) or in-structure response spectra (ISRS) as the earthquake input at the base of the equipment. The amplitude of the FRS may be noticeably reduced when obtained from coupling analysis because of interaction between the primary structure and the equipment. This paper introduces a method using a modal synthesis approach to generate the FRS in a coupled primary-secondary system that can avoid numerical instabilities or inaccuracies. The FRS were generated by considering the dynamic interaction that can occur at the interface between the supporting structure and the equipment. This study performed a numerical example analysis using a typical nuclear structure to investigate the coupling effect when generating the FRS. The study results show that the coupling analysis dominantly reduces the FRS and yields rational results. The modal synthesis approach is very practical to implement because it requires information on only a small number of dynamic characteristics of the primary and the secondary systems such as frequencies, modal participation factors, and mode shape ordinates at the locations where the FRS needs to be generated.

• 생명과학회지
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• 제16권7호
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• pp.1097-1103
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• 2006

Community structure varies not only in space but also in time. We stand in one position which located at Sinhung-ri, Sacheon-ci and observe the flora of area as time passes. This area begins after disturbance on sites where organisms are already present like secondary succession. In 2001, there are invaded by Trapa japonica, Salvinia natans, and Potamogon cristatus. Four or five years later, this abandoned areas support of clover, pine, and oak, resulting in a shifting pattern of species dominance and diversity through time. Patterns of community structure such as species composition and ecological diversity have shown through seasons and five years, that is the topic of this study. The values of turnover (TO) were changes through time intervals at three regions. The gradual and seemingly directional change in the structure of the community through time from aquatic like to field. Thus, we can observe the process of secondary succession at Sinhung-ri in the very short time.

• 한국자기공명학회논문지
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• 제21권2호
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• pp.50-54
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• 2017

Cupin-superfamily proteins represent the most functionally diverse groups of proteins and include a huge number of functionally uncharacterized proteins. Recently, YaiE, a cupin protein from Escherichia coli has been suggested to be involved in a novel activity of pyrimidine/purine nucleoside phosphorylase (PPNP). In the present study, we achieved a complete backbone NMR assignments of YaiE, by a series of heteronuclear multidimensional NMR experiments on its [$^{13}C/^{15}N$]-enriched sample. Subsequently, secondary structure analysis using the assigned chemical shift values identified 10 obvious ${\beta}-strands$ and a tentative $3_{10}-helix$. Taken all together, the results constitute the first structural characterization of a putative PPNP cupin protein.