• 한국자기공명학회논문지
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• 제5권1호
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• pp.37-45
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• 2001

Synthetic pulmonary surfactants consisting of a mixture of phospholipids with synthetic peptides based on human surfactant-associated protein SP-B were prepared. These surfactants were analyzed f3r their secondary structures by circular dichroism (CD) spectroscopy and NMR spectroscopy. Two synthetic peptides (SP-B(3), SP-B(4)) combined with the phospholipid mixture displayed significant surfactant properties. The CD spectra showed that the u-helical propensities of the peptides in DPC micelles. In the NMR spectroscopy, the tertiary structures of SP-B(3) show that it has $\alpha$-helical structure from Gln5 to Arg13 in DPC micelle and SP-B(4) show that they have $\alpha$-helical structure from Gln5 to Leu12 in DPC micelle. Based on these structures, truncated peptides originated from SP-B protein, can be designed as effective synthetic surfactants for clinical use.

• Molecules and Cells
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• 제24권1호
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• pp.27-36
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• 2007

The hypothetical protein TTC0263 of Thermus thermophilus HB27 is a thermophilic tetratricopeptide repeat (TPR)-containing protein. In the present study, the TPR region (residues 26-230) was resolved at $2.5{\AA}$ with R-factors of $R/R_{free}$ = 23.6%/28.6% $R/R_{free}=23.6%/28.6%$. TTC0263 consists of 11 helices that form five TPR units. Uniquely, it contains one atypical "extended" TPR (eTPR) unit. This comprises extended helical residues near the loop region of TTC0263, such that the helical length of eTPR is longer than that of the canonical TPR sequence. In addition, the hybrid TPR domain of TTC0263 possesses oligomer-forming characteristics. TPR domains are generally involved in forming multi-subunit complexes by interacting with each other or with other subunit proteins. The dynamic structure of TTC0263 described here goes some way to explaining how TPR domains mediate the formation of multi-subunit complexes.

• Journal of applied mathematics & informatics
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• 제12권1_2호
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• pp.155-164
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• 2003

A method is proposed to predict the distances between given residue pairs (between C$\sub$${\alpha}$/ atoms) of a protein using a sequence to structure mapping by indefinite quadratic approximation. The prediction technique requires a data fitting in three dimensional space with coordinates of the residues of known structured proteins and leads to a numerical ref resentation of 20 amino acids by minimizing a large least norm iteratively. These approximations are used in distance prediction for given residue pairs. Some computational experience on a test set of small proteins from Brookhaven Protein Data Bank are given.

• 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.

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 2002년도 International Symposium on Magnetic Resonance
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• pp.76-76
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• 2002

• 생명과학회지
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• 제11권1호
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• pp.43-47
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• 2001

A mutant tryptophan synthase $\alpha$-subunit, where Pro28 was replaced with Leu, tends to be expressed in recombinant E. coli. CD and fluorescence spectra of this protein indicate some changes in secondary and tertiary structure. Wild type protein was more or less affected by {TEX}$Ca^{2+}${/TEX} ion in regards of the fluorescent properties of its native, unfolded and intermediate forms, but the mutant protein was not at all. The dramatic structural changes may be related to the aggregation of this mutant protein.

• 한국자기공명학회:학술대회논문집
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• 한국자기공명학회 2002년도 제20회 학술발표회
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• pp.25-25
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• 2002

• 한국자기공명학회논문지
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• 제26권4호
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• pp.66-70
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• 2022

Protein structure determination using NMR spectroscopy requires a suite of heteronuclear 3-D NMR experiments that can take a couple of weeks for completion. During the experiments, protein samples may suffer from slow degradation due to co-purifying proteases, which complicates and slows down the assignment procedure. Here we describe a practical protocol to avoid unwanted proteolysis during the experiment.

• Korean Chemical Engineering Research
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• 제46권3호
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• pp.529-534
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• 2008

생체복합재료인 참굴 (Crassostrea gigas) 패각은 생성되는 형태에 따라 정상패각과 재생패각으로 구분되었다. 산과 알칼리를 이용한 탈 석회화과정 및 단백질제거반응을 통해 재생패각 내에서 얻어진 유기막이 키틴 특성을 가지고 있음을 FT-IR (Fourier transform infrared spectrometer)과 XRD (X-ray Diffractometer)를 통해 확인하였다. 불용성단백질의 함량은 정상패각이 재생패각과 비교하여 두배 이상 이었던 반면 수용성단백질 2차구조는 재생패각의 경우 random과 같은 불규칙구조가 많은 부분을 차지하고 있음을 확인할 수 있었다. 수용성단백질의 아미노산 조성과 단백질 2차구조분석을 통해 재생패각의 탄산칼슘 합성전략을 분자수준에서 논의하였고 재생패각 형성과 관련된 생광물화 전략이 패각의 재료학적 특성에 미치는 결과로써 해석되었다.

• Journal of Plant Biotechnology
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• 제1권1호
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• pp.13-19
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• 1999

The visco-elastic properties of gluten are major determinants of the processing properties of doughs. These visco-elastic properties are strongly influenced by the ratio of monomeric and polymeric proteins and the size distribution of the polymeric proteins, which make up the gluten fraction of the dough. Recent studies have revealed that other features, such as the number of the cysteine residues of the HMW-GS, also play an important role in determining the functional characteristics. To modify the processing properties at molecular level, the relationship between the structure of molecules and dough properties has to be understood. In order to explore the relationships between individual proteins and dough properties, we have developed procedures for incorporating bacterially expressed proteins into doughs, and measuring their functional properties in small-scale equipment. A major problem in investigating the structure/function relationships of individual seed storage proteins is to obtain sufficient amounts of pure polypeptides from the complex families of proteins expressed in the endosperm. Therefore, we have established a simplified model system in which we produce specific protein genes through bacterial expression and test their functional properties in smallscale apparatus after incorporation into base flour. An S poor protein gene has been chosen as a template gene. This template gene has been modified using standard recombinant DNA techniques in order to test the effects of varying the number and position of cysteine residues, and the size of the protein. Doughs have been mixed in small scale apparatus and characterized with respect to their polymeric composition and their functional properties, including dough mixing, extensibility and small scale bating. We conclude that dough characteristics can be manipulated in a predictable manner by altering the cysteine residues and the size of high molecular weight glutenins.