• Bulletin of the Korean Chemical Society
• /
• 제30권12호
• /
• pp.3006-3010
• /
• 2009

We have performed long time REMD simulation on 15-19 residues of human calcitonin hormone (DFNKF) which is known to form highly ordered amyloid fibril. The simulation started from randomly oriented multiple DFNKF strand. Using all-atom level simulations with the generalized Born solvation (GB) model (param99MOD3), we observed spontaneous formation of ${\beta}$-sheet for tetramer. Interestingly, the current simulation gives anti-parallel sheet as a major conformation, consistent with experiments. The major interaction stabilizing the anti-parallel sheet seems to be the inter-strand hydrogen bond.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제20권2호
• /
• pp.87-91
• /
• 2010

Silk fibroin model peptide, alanine pentamer was synthesized through solid-phase method and modified with poly(ethylene glycol). Nuclear magnetic resonance spectrometry and Fourier-transform infrared spectroscopy showed the conformation of alanine pentamer, $\beta$-sheet structure and random coil conformation were not changed with PEGylation. Differential scanning calorimetry showed that relatively strong exothermic peak around $180^{\circ}C$ by PEGylation. No cytotoxicity of PEGylated pentamer was observed by L929 cell proliferation test.

• BMB Reports
• /
• 제33권2호
• /
• pp.133-137
• /
• 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
• /
• 제33권3호
• /
• pp.848-854
• /
• 2012

We have studied the oligomerization of a fibril-forming segment of ${\alpha}$-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of ${\alpha}$-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel ${\beta}$-sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.

• BMB Reports
• /
• 제33권5호
• /
• pp.379-384
• /
• 2000

The native conformation of serpins (serine protease inhibitors) is strained. Upon cleavage of the reactive center loop of serpins by a protease, the amino terminal portion of the cleaved loop is inserted into the central ${\beta}-sheet$, A sheet, as the fourth strand, with the concomitant release of the native strain. We questioned the role of protease in this conformational switch from the strained native form into a stable relaxed state. Chemical cleavage of the reactive center loop of ${\alpha}_1-antitrypsin$, a prototype serpin, using hydroxylamine dramatically increased the stability of the serpin. A circular dichroism spectrum and peptide binding study suggests that the amino terminal portion of the reactive center loop is inserted into the A sheet in the chemically-cleaved ${\alpha}_1-antitrypsin$, as in the enzymatically-cleaved molecule. These results indicate that the structural transformation of a serpin molecule does not require interaction with a protease. The results suggest that the serpin conformational switch that occurred during the complex formation with a target protease is induced by the cleavage of the reactive center loop per se.

• 한국잠사곤충학회지
• /
• 제39권2호
• /
• pp.186-196
• /
• 1997

The IR crystallinity index of Calcium nitrate treated silk fiber decreased proportionally to the concentration of calcium nitrate. A partial change of conformation was observed in the concentration of over 46.4-47.6% changing from $\beta$-sheet or to random coil in the crystalline region. This is in coincidence with the result of crystallinity index, which was started to be reduced in the concentration range of 46.4-47.6%. A same trend was observed for the X-ray order factor, birefringence, degree of orientation and surface structure. These structural parameters were remarkably changed on the treatment of silk fibers with concentration of 46.4-17, 6% calcium nitrate. Therefore, it seems that there exists a critical concentration of calcium nitrate in affection the structure and morphology of silk fibers. According to the examination of surface morphology, the fine stripe was observed in the direction of fiber axis at 46.4% concentration. However, the treated concentration was exceeded by 47.6%, the cracks were appeared severely on the fiber surface in the transverse direction as well as fiber axis direction. This result might be related to the tensile properties, specially a tenacity of silk fibers. As a result of quantitative analysis of a dilute acid hydrolysis, three different regions, which are known as a amorphous, semi-crystalline and crystalline region, could be obtained. The hydrolysis rate curves were different with various concentrations of treatment and the relative contents of each region could be calculated.

• 한국잠사곤충학회지
• /
• 제42권2호
• /
• pp.114-119
• /
• 2000

Effects of ethanlo treatment on the structural and thermal characteristics of regenerated Antheraea pernyi silk fibroin (RSF) were investigated. Infrared spectroscopy and X-ray diffractometry showed that the conformational transition of RSF might be affected by concentration of ethanol and its treatment time. The structure of RSF was rapidly changed from random coil to $\beta$-sheet conformation when RSF was treated with les than 75% ethanol concentration. However, RSF treated with ethanol(100%) did not show conformational change. Differential scanning calorimetry showed that exotherm at 232$\^{C}$ disappeared and the intensity of endotherm at 228$\^{C}$ decreased with treatment of 75% ethanol. Dynamic thermal analysis showed that loss modulus (E") and tan $\delta$$\_$E/ of RSF treated with aqueous ethanol was broaden and shifted to higher temperature in comparison with those of untreated RSF.

• Macromolecular Research
• /
• 제16권7호
• /
• pp.604-608
• /
• 2008

Color dye-doped silk fibroin nanoparticles were successfully fabricated using a microemulsion method. An aqueous silk fibroin solution was prepared by dissolving cocoons (Bombyx mori) in a concentrated lithium bromide solution followed by dialysis. A color dye solution was also mixed with the aqueous silk fibroin solution. The surfactants used for the microemulsion were then removed by methanol and ethanol, yielding color dye-doped silk fibroin nanoparticles, approximately 167 nm in diameter. The secondary structure of the nanoparticles showed a $\beta$-sheet conformation, as characterized by Fourier transform infrared spectroscopy. The morphology of the nanoparticles was determined by field emission scanning electron microscopy, transmission electron microscopy and atomic force microscopy, and their size and size distribution were measured by dynamic light scattering. The color dye-doped silk fibroin nanoparticles were examined by confocal laser scanning microscopy.

• 한국잠사곤충학회지
• /
• 제46권1호
• /
• pp.28-31
• /
• 2004

견피브로인의 응용가능성을 높이기 위하여 대표적인 생체고분자인 히아론산을 이용하여 견피브로인/히아론산 브렌드 필름을 제조하였으며 구조 및 열 특성을 살펴보았다. 1. 적외선 분광분석 결과 견피브로인과 히아론산 두 고분자 사이에는 수소결합 등의 상호작용이 존재하지 않는 것으로 나타났다. 또한 브렌드 필름내에 존재하는 실크피브로인은 EDC 에탄올 용액처리에 의하여 $\beta$-sheet 구조로 전이되었다. 2. 견피브로인/히아론산 브렌드 필름에서 견피브로인과 히아론산 각각의 열분해 흡열피크와 발열피크 온도에는 큰 변화가 없었으나, 열분해 피크의 폭이 넓어지는 것으로 봐서 실크 피브로인과의 브렌드 또는 EDC 처리에 의하여 열분해 반응이 매우 복잡한 환경하에서 진행되고 있음을 알 수 있었다. 3 견피브로인/히아로산 브렌드 필름은 자기 중량 대비 평균 70배의 수분을 흡수하였다.

• BMB Reports
• /
• 제39권3호
• /
• pp.284-291
• /
• 2006

In this study, the cDNA of a new peptide from the venom of the scorpion, Buthotus saulcyi, was cloned and sequenced. It codes for a 64 residues peptide (Bsaul1) which shares high sequence similarity with depressant insect toxins of scorpions. The differences between them mainly appear in the loop1 which connects the $\beta$-strand1 to the $\alpha$-helix and seems to be functionally important in long chain scorpion neurotoxins. This loop is three amino acids longer in Bsaul1 compared to other depressant toxins. A comparative amino acid sequence analysis done on Bsaul1 and some of $\alpha$-, $\beta$-, excitatory and depressant toxins of scorpions showed that Bsaul1 contains all the residues which are highly conserved among long chain scorpion neurotoxins. Structural model of Bsaul1 was generated using Ts1 (a $\beta$-toxin that competes with the depressant insect toxins for binding to $Na^+$ channels) as template. According to the molecular model of Bsaul1, the folding of the polypeptide chain is being composed of an anti-parallel three-stranded $\beta$-sheet and a stretch of $\alpha$-helix, tightly bound by a set of four disulfide bridges. A striking similarity in the spatial arrangement of some critical residues was shown by superposition of the backbone conformation of Bsaul1 and Ts1.