• Proceedings of the Korean Information Science Society Conference
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• 2003.04a
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• pp.890-892
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• 2003

단백질 구조의 표현 방법을 정형화하고 호환성 및 상호작용성을 향상하기 위하여 단백질의 이차구조 구성요소와 그들 사이의 관계를 이용하여 단백질 구조를 기술하는 PSA가 제안되었다. 본 논문에서는 PSA에서 정의된 단백질의 이차구조 사이에 정의된 요소 중에서 네 가지의 각도관계와 다섯 가지의 거리관계를 계산하는 방법에 대하여 기술하였으며, 이를 자바로 구현하여 그 결과를 확인하였다. 본 논문에서 제안한 방법은 단백질의 이차구조 사이의 상관관계를 포함하는 PSAML 데이터로부터 단백질의 구조 및 유사성을 비교하기 위한 단백질 구조비교 시스템에서 사용할 수 있다.

• Mycobiology
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• v.37 no.4
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• pp.286-294
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• 2009

Heteropolysaccharides isolated from liquid cultures of nine Tremella species contained 0.3 to 1.2% protein, 2.7 to 5% ash, 0.9 to 3.4% acetyl groups, 76.5 to 84.2% carbohydrates and trace amounts of starch. The polysaccharides in aqueous solution were slightly acidic (pH 5.1 to 5.6). They consisted of the following monomeric sugars: fucose, ribose, xylose, arabinose, mannose, galactose, glucose and glucuronic acid. The backbones of the polysaccharide structures consisted of $\alpha$-(1$\rightarrow$3)-links while the side chains were $\beta$-linked.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.224-233
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• 2012

The limiting sequence and relative ratio of lysine (Lys), methionine (Met), and threonine (Thr) for calves about 2 mo of age fed milk replacers (MR) containing soy protein are not clearly defined. The objective of the study was to investigate the effect of supplementing MR containing 22% CP, half from soy protein concentrate (SPC, 40.56% CP, flour) and half from whey proteins, with Lys, Met, and Thr to estimate amino acid (AA) sequence and their relative ratio for calves about 2 mo of age. A method of partial deduction of AA was adopted. Twenty-four newborn calves (half males and half females, $40.7{\pm}0.9$ kg of BW) were fed 1 of 4 MR diets for 56 d (n = 6/diet). The diets were supplemented with all (positive control) or with 2 of the 3 AAs: Lys, Met and Thr, (i.e., PC (22% CP, 2.34% Lys, 0.72% Met and 1.80% Thr), PC-Lys (22% CP, 1.64% Lys, 0.72% Met and 1.80% Thr), PC-Met (22% CP, 2.34% Lys, 0.50% Met and 1.80% Thr), and PC-Thr (22% CP, 2.34% Lys, 0.72% Met and 1.26% Thr)). Calves were fed thrice daily; starter (20% CP, 1.03% Lys, 0.30% Met and 0.69% Thr), hay (3.23% CP, 0.29% Lys, 0.12% Met and 0.23% Thr) and water were offered free choice. Starter and hay were only offered beginning on d 36 (after 5 wk) and d 43 (after 6 wk), respectively. BW, body size and blood samples measures were taken every two weeks. Three-day total collection of feed refusals, feces, and urine were recorded starting at d 33 and d 54 of age, respectively. From the results, the limiting sequence and relative ratio between the 3 AAs in calves with different diet structures were calculated. The limiting sequence of the 3 AAs were ranked as Lys, Met and Thr; the proper ratio was 100:29:70 for MR-only diet and 100:30:60 for diets consisted of MR, starter and hay. Nitrogen digestion and utilization and nutrient digestibility were negatively affected by AA deletion treatments. From the evidence of this experiment, it did not appear that the AA limiting sequence was selectively altered by differences in diet structures such as would be encountered in practice. The relative ratio between the 3 AAs varied with the offer of starter and hay to calves, and the average ratio was 100:29.5:65 for calves during 2 to 10 wk of age.

• Korean Journal of Food Science and Technology
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• v.30 no.6
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• pp.1350-1356
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• 1998

An attempt was made to investigate the effects of additives (3%) such as egg white, soybean protein, corn starch and Read Amity-N (green bean starch 85%+psyllium husk 10%) on the thermal properties and gel structures of mackerel surimi and to examine the quality of surimi by using differential scanning calorimetry (DSC), rheometry and scanning electron microscopy (SEM). The thermal transition temperatures of mackerel surimi protein were 40, 52, 67 and $79^{\circ}C$ after those temperatures were changed to 37, 46, 57 and $76^{\circ}C$ after adding salt (3% NaCl). Addition of Read Amity-N and corn starch to surimi showed new peak at the temperature of $90^{\circ}C\;and\;92^{\circ}C$, respectively. The enhancing effects of gel strengths of mackerel surimi cooked gels prepared from adding four kinds of additives, respectively, were egg white > soybean protein > Read Amity-N > corn starch in order. Scanning electron microscopy showed a difference in fine structures between the cooked gels which were prepared with and without additives. Dispersion profiles of protein were more thick in cooked gel prepared with additive than in cooked gel prepared without additive.

• Development and Reproduction
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• v.4 no.1
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• pp.67-77
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• 2000

Snailfish usually lives at the bottom of the sea and showed typical retrogressive change with specialized tissue structures of skin and skeletons. In order to obtain the specific genes of snailfish, highly expressed in the body, we made subtracted cDNA library and analyzed 200 clones. Totally 200 clones were obtained and sequenced, and among them 62 clones were turned out to be homologous to the known gene, i.e., thioesterase (9), myosin (8), creatine kinase (7), skeletal alpha-actin (6), parvalbumin b (5), ribosomal protein (5), type I collagen (3), muscle troponin (3), dopamine receptor (2), histatin (2), and heat shock protein (2), cystatin (1), lectin (1), statherin (1), secretory carrier membrane protein (1), keratin type I (1), desmin (1), chloroplast (1), muscle tropomyosin (1), reticulum calcium ATPase (1), ribonucleoprotein (1). The remaining 138 clones were low homologous or non-redundant genes through Genbank search. Especially 5 clones were novel and specifically expressed in the body tissues of Snailfish by in situ hybridization. Therefore, we analysed these 5 clones to identify the C-terminal protein structures and motifs, and partly defined the roles of these proteins in comparison with the expression patterns by in situ hybridization. C9O-77, about 5000 bp, was supposed to be a matrix protein expressed strongly positive in epithelium, myxoid tissue, fibrous tissue and collagenous tissue. C9O-116, about 1500 bp, was supposed to be a transmembrane protein which was weakly expressed in the fibrous tissue, epithelium tissue, and myxoid tissue, but strong in muscle tissue. C9O-130, about 1200 bp, was supposed to be an intracytoplasmic molecule usually in the epithelial cells. C9O-161, about 2000 bp, was weakly expressed in epithelium, muscle tissue and myxoid tissue, but specially strong in epithelium. C9O-171, about 1000 bp, was supposed to be a transcription factor containing zinc finger like domain, which was intensely expressed in the epithelium, muscle tissue, fibrous tissue, and in collagenous tissue.

• Journal of Life Science
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• v.19 no.2
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• pp.284-288
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• 2009

The innate immune system is important for the first line of host defence against infectious agents, which have penetrated the mechanical barriers. Mannose-binding lectin (MBL or mannan-binding protein, MBP) is a serum protein that is synthesized in the liver as a part of the acute phase response. MBL binds to carbohydrate structures presented by a wide range of pathogenic bacteria, viruses, fungi, and parasites. MBL is synthesized as a monomer that has a carboxy-terminal carbohydrate recognition domain, a neck region and a collagen region. Low MBL level was reported to be the most frequent immuno-deficiency syndrome. Although extensive studies have yielded detailed information on the structure of MBL, functions of the MBL complex are not fully understood yet. We, here, present cloning process of MBL cDNA from the rat liver and production of truncated recombinant MBL protein using a bacterial expression system in order to produce anti-MBL polyclonal antibody. Anti-MBL polyclonal antibody was raised in a New Zealand rabbit and its affinity was tested against recombinant protein using western blot technique. MBL cDNA, recombinant protein and anti-MBL antibody could be used as great arsenals to dissect cellular biochemistry of MBL.

• Journal of Photoscience
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• v.9 no.2
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• pp.534-536
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• 2002

A halophilic archaeon, Halobacterium salinarum, exhibits phototactic behaviors, by which the organism is guided to red-orange light and evades shorter wavelengths of light. The phototaxis is mediated by two retinal proteins, sensory rhodopsin I and II (SRI and SRII), whose structures are analogous to the cognate protein bacteriorhodopsin, a light-driven proton pump. SRI mediates both attractant and repellent swimming behaviors to orange light and near- UV light, respectively. The two different signaling through the single photoreceptor have been ascribed to the presence of two active structures of SRI (S$\_$373/ and P$\_$520), which are produced upon orange light illumination of SRI and upon subsequent near-UV illumination of S$\_$373/, respectively. In the present study, we have measured the difference FTIR spectra of S$\_$373/ and P$\_$520/ states. In P$\_$520/, the isomeric structure of the chromophore is assignable to all-trans, and the Schiff base of the chromophore is protonated with concomitant deprotonation of Asp76, a combination which allows for the formation of a salt bridge between them. It was suggested that the way of interaction between the Schiff base and the counterion, which is different among SRI$\_$587/, S$\_$373/ and P$\_$520/ and which has been shown to drive the conformational changes in the cognate protein, bacteriorhodopsin, is the key to controlling conformational changes for the attractant and the repellent signaling by SRI.

• Molecules and Cells
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• v.27 no.6
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• pp.651-656
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• 2009

The formation of ${\beta}$-amyloid peptide ($A{\beta}$) is initiated from cleavage of amyloid precursor protein (APP) by a family of protease, ${\alpha}$-, ${\beta}$-, and ${\gamma}$-secretase. Sub W, a substrate peptide, consists of 10 amino acids, which are adjacent to the ${\beta}$-cleavage site of wild-type APP, and Sub M is Swedish mutant with double mutations on the left side of the ${\beta}$-cleavage site of APP. Sub W is a normal product of the metabolism of APP in the secretary pathway. Sub M is known to increase the efficiency of ${\beta}$-secretase activity, resulting in a more specific binding model compared to Sub W. Three-dimensional structures of Sub W and Sub M were studied by CD and NMR spectroscopy in water solution. On the basis of these structures, interaction models of ${\beta}$-secretase and substrate peptides were determined by molecular dynamics simulation. Four hydrogen bonds and one water-mediated interaction were formed in the docking models. In particular, the hydrogen bonding network of Sub M-BACE formed spread over the broad region of the active site of ${\beta}$-secretase (P5-P3'), and the side chain of P2- Asn formed a hydrogen bond specifically with the side chain of Arg235. These are more favorable to the cleavage of Sub M by ${\beta}$-secretase than Sub W. The two substrate peptides showed different tendency to bind to ${\beta}$-secretase and this information may useful for drug development to treat and prevent Alzheimer's disease.

• Journal of Life Science
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• v.9 no.4
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• pp.473-480
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• 1999

This study was designed to investigate the effects of pine (Pinus densiflora Sieb et Zucc) needle extract (PNE) on membrane fluidity and oxidative stress in liver membranes of Sprague-Dawley (SD) rats as a study on investigation of anti-aging effect and determination of chemical structures of PNE through the animal experiments. Male SD rats were fed basic diets (control group) and experimental diets (0.5% and 1.0%-PNE group) for 6 weeks. Administrations of 0.5% and 1.0%-PNE resulted in a marked decreases (15∼25% and 23∼26%, respectively) in cholesterol accumulations of liver mitochondria and microsomes compared with control group. Membrane fluidities were significantly increased (15∼25%) in liver microsomes of 0.5% and 1.0%-PNE groups compared with control group. Formations of basal and induced oxygen radicals (BOR and IOR) in liver mitochondria were significantly inhibited (11∼12% and 10∼15%, respectively) by administrations of 0.5% and 1.0%-PNE compared with control group. Lipid peroxide (LPO) levels were remarkbly decreased about 20% in liver mitochondria and microsomes of 0.5% and 1.0%-PNE groups compared with control group. Oxidized protein levels calculated with carbonyl group were significantly decreased about 15% in liver mitochondria of 1.0%-PNE group compared with control group. These results suggest that PNE may play a effective role in a attenuating a oxidative stress and increasing a membrane fluidity.

• Journal of the Korean Magnetic Resonance Society
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• v.13 no.1
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• pp.27-34
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• 2009

HP (2-20), a 19-residue peptide derived from the N-terminus of Helicobacter pylori Ribosomal Protein L1, has antimicrobial activity but is not cytotoxic to human erythrocytes. Previously, we have synthesized several analogue peptides to investigate the effects of substitutions on the structure and antimicrobial activity. Substitution of $Gln^{16}$ and $Asp^{18}$ with Trp (Anal 3) caused a dramatic increase in bacterial and fungal lytic activities. In this study, analogue peptides were synthesized to investigate the effects of substitution of Gin and Asp with Phe (Anal 6) or Tyr (Anal 7) in HP (2-20) on its structure and antimicrobial activity. Substitution of Gin and Asp with hydrophobic aromatic residues at position 16 and 18 of HP (2-20) caused increase in antibiotic activity without hemolytic effect. Substitution of Gin and Asp with Trp and Try increased antibiotic activity of HP (220) twice more compared to substitution with Phe. The tertiary structures of Anal 6 and Anal 7 in SDS micelles has been investigated using NMR spectroscopy. The structures revealed that substitutions of the aromatic residues at C-terminus resulted in longer and well defined alpha-helix and improved their antibacterial activities