• Proceedings of the Korea Information Processing Society Conference
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• 2003.11b
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• pp.821-824
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• 2003

단백질의 이차구조 중에서 ${\beta}-sheet$의 구조를 비교하는데 있어서 비정확성의 문제가 있다. 이는 ${\beta}-sheet$가 그 구조적 특성 때문에 휘어지기 때문이다. 그래서 본 논문에서는 PSA에서 정의된 ${\beta}-sheet$를 좀 더 적절하게 추상화하기 위해서 ${\beta}-sheet$를 분할하는 방법을 제안하였으며 이 방법을 DOM을 이용하여 JAVA로 구현하였다. 본 논문에서 제안한 방법은, 단백질의 이차구조의 정보를 포함하는 PSAML 데이터로부터 단백질의 구조 및 유사성을 비교하기 위한 단백질 구조비교 시스템에서 사용할 수 있다.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.8
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• pp.1159-1165
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• 2016

The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller's dried grains with solubles, corn gluten meal, and feather meal by Fourier transform infrared (FTIR) spectroscopy to determine the protein molecular spectral band characteristics for amides I and II as well as ${\alpha}$-helices and ${\beta}$-sheets and their ratios. Protein solubility and in vitro digestibility were measured with the Kjeldahl method using 0.2% KOH solution and the pepsin-pancreatin two-step enzymatic method, respectively. We found that all measured spectral band intensities (height and area) of feed proteins were correlated with their the in vitro digestibility and solubility ($p{\leq}0.003$); moreover, the relatively quantitative amounts of ${\alpha}$-helices, random coils, and ${\alpha}$-helix to ${\beta}$-sheet ratio in protein secondary structures were positively correlated with protein in vitro digestibility and solubility ($p{\leq}0.004$). On the other hand, the percentage of ${\beta}$-sheet structures was negatively correlated with protein in vitro digestibility (p<0.001) and solubility (p = 0.002). These results demonstrate that the molecular structure characteristics of feed proteins are closely related to their in vitro digestibility at 28 h and solubility. Furthermore, the ${\alpha}$-helix-to-${\beta}$-sheet ratio can be used to predict the nutritional value of feed proteins.

• BMB Reports
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• v.40 no.1
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• pp.58-64
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• 2007

Similar to the other known structures of Bacillus thuringiensis Cry $\delta$-endotoxins, the crystal structure of the 65-kDa activated Cry4Ba toxin comprises three domains which are, from the N- to C-terminus, a bundle of $\alpha$-helices, a three-$\beta$-sheet domain, and a $\beta$-sandwich. To investigate the properties of the C-terminal domain III in isolation from the rest of the toxin, the cloned Cry4Ba-domain III was over-expressed as a 21-kDa soluble protein in Escherichia coli, which cross-reacted with anti-Cry4Ba domain III monoclonal antibody. A highly-purified domain III was obtained in a monomeric form by ion-exchange and size-exclusion FPLC. Circular dichroism spectroscopy indicated that the isolated domain III fragment distinctly exists as a $\beta$-sheet structure, corresponding to the domain III structure embodied in the Cry4Ba crystal structure. In vitro binding analysis via immuno-histochemical assay revealed that the Cry4Ba-domain III protein was able to bind to the apical microvilli of the susceptible Stegomyia aegypti larval midguts, albeit at lower-binding activity when compared with the full-length active toxin. These results demonstrate for the first time that the C-terminal domain III of the Cry4Ba mosquito-larvicidal protein, which can be isolated as a native folded monomer, conceivably participates in toxin-receptor recognition.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1225-1228
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• 2005

C-terminal fragments of APP (APP-CTs), that contain A$\beta$ sequence, are found in neurotic plaques, neurofibrillary tangles and the cytosol of lymphoblastoid cells obtained from AD patients. CT26, Thr639-Asp664 (TVIVITLVMLKKKQYTSIHH GVVEVD) includes not only the transmembrane domain but also the cytoplasmic domain of APP. This sequence is produced from cleavage of APP by caspase and $\gamma$-secretase. In this study, the solution structure of CT26 was investigated using NMR spectroscopy and circular dichroism (CD) spectropolarimeter in various membrane-mimicking environments. According to CD spectra and the tertiary structure of CT26 determined in TFE-containing aqueous solution, CT26 has an α-helical structure from $Val^{2}\;to\;Lys^{11}$ in TFE-containing aqueous solution. However, according to CD data, CT26 adopts a $\beta$-sheet structure in the SDS micelles and DPC micelles. This result implies that CT26 may have a conformational transition between $\alpha$-helix and $\beta$-sheet structure. This study may provide an insight into the conformational basis of the pathological activity of the C-terminal fragments of APP in the model membrane.

• BMB Reports
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• v.33 no.2
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• pp.133-137
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• 2000

To elucidate the effect of oxygen radicals on the molecular properties of proteins, the secondary and tertiary structure and molecular weight size of BSA and ${\beta}$-lactoglobulin were examined after irradiation of proteins at various doses. Gamma-irradiation of protein solutions caused the disruption of the ordered structure of protein molecules as well as degradation, cross-linking, and aggregation of the polypeptide chains. As a model system, BSA and ${\beta}$-lactoglobulin were used as a typical ${\alpha}$-helical and a ${\beta}$-sheet structure protein, respectively. A circular dichroism study showed that the increase of radiation decreased the ordered structure of proteins with a concurrent increase of aperiodic structure content. Fluorescence spectroscopy indicated that irradiation quenched the emission intensity excited at 280 nm. SDS-PAGE and a gel permeation chromatography study indicated that radiation caused initial fragmentation of proteins resulting in a subsequent aggregation due to cross-linking of protein molecules.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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• pp.1845-1850
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• 2009

We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of $\alpha$-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields- AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel $\beta$-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial $\beta$-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.237-249
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• 2014

Deposition of amyloid-${\beta}$ ($A{\beta}$) proteins is the conventional pathological hallmark of Alzheimer's disease (AD). The $A{\beta}$ protein formed from the amyloid precursor protein is predominated by the 40 residue protein ($A{\beta}40$) and by the 42 residue protein ($A{\beta}42$). While $A{\beta}40$ and $A{\beta}42$ differ in only two amino acid residues at the C-terminal end, $A{\beta}42$ is much more prone to aggregate and exhibits more neurotoxicity than $A{\beta}40$. Here, we investigate the molecular origin of the difference in the aggregation propensity of these two proteins by performing fully atomistic, explicit-water molecular dynamics simulations. Then, it is followed by the solvation thermodynamic analysis based on the integral-equation theory of liquids. We find that $A{\beta}42$ displays higher tendency to adopt ${\beta}$-sheet conformations than $A{\beta}40$, which would consequently facilitate the conversion to the ${\beta}$-sheet rich fibril structure. Furthermore, the solvation thermodynamic analysis on the simulated protein conformations indicates that $A{\beta}42$ is more hydrophobic than $A{\beta}40$, implying that the surrounding water imparts a larger thermodynamic driving force for the self-assembly of $A{\beta}42$. Taken together, our results provide structural and thermodynamic grounds on why $A{\beta}42$ is more aggregation-prone than $A{\beta}40$ in aqueous environments.

• Journal of Sericultural and Entomological Science
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• v.42 no.1
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• pp.42-47
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• 2000

Structural and thermal characteristics of silk fibroin/poly(2-hydroxyethyl methacrylate)(PHEMA) blend films were investigated using FTIR, X-ray diffractometer, differential scanning calorimeter, thermogravimeter and scanning electron microscope. FTIR spectra showed that the conformation of silk fibroin prepared by dissolving in formic acid was $\beta$-sheet, which did not affected by blending with PHEMA. The X-ray diffraction patterns also showed that individual crystalline structure of silk fibroin and PHEMA was not affected for the blend films. The initial thermal decomposition temperature of silk fibroin/PHEMA blend film tends to be higher than either of silk fkbroin or PHEMA. Thermal stability of both polymers, more notably PHEMA, can be improved by blending two components. As a result of SEM observation, the phases separation for silk fibroin/PHEMA blend films occured regardless of blend ratio ; continuous and dispersed phase were silk fibroin and PHEMA component, respectively.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.159-161
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• 2002

Bacteriophage lambda integrase carries out the site-specific recombination of lambda. Integrase contains two DNA binding domains with distinct sequence specificity, namely arm-type binding and core-type binding domains. The amino-terminal arm-binding domain is structurally related to the three-stranded $\beta-sheet$ family of DNA-binding domains. Integrase binding to the high affinity arm-type site by the amino-terminal domain facilitates Int binding to the low affinity core-type site, where the cleavage and strand exchange occurs. The amino-terminal domain of Int also modulates the core-binding and catalysis through intramolecular domain-domain interaction and/or intermolecular interactions between Int monomers. In addition, the amino-terminal domain interacts cooperatively with excisionase during excision. This indicates that amino-terminal domain of Int plays an important role in formation of proper higher-order nucleoprotein structure required for lambda site-specific recombination.

• International Journal of Industrial Entomology and Biomaterials
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• v.38 no.2
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• pp.51-55
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• 2019

The structure and properties of silk polymers (fibroin and sericin) can be satisfactorily controlled by choosing a suitable silkworm variety and, hence, this parameter (i.e., silkworm variety) has attracted increasing attention. A previous study reported that the crystallinity of white colored silkworm cocoons depends on the silkworm variety. In the present study, sixteen yellow colored silkworm variety cocoons were produced and their molecular conformation and crystallinity were investigated. The conformation of the silkworm cocoons varied with the silkworm variety. Most cocoons exhibited ${\beta}$-sheet conformation, although random coil and ${\beta}$-sheet conformations co-existed in some cocoons (e.g., 21 and D90). The crystallinity of the silkworm cocoons varied with the silkworm variety and the measurement position of the cocoon (i.e., outer surface or inner surface). However, the difference in the crystallinity indices of the outer and inner surfaces comprising the cocoons varied with the silkworm variety, but was <2% for all cocoons, except for MAL.