• 한국환경과학회지
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• 제12권1호
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• pp.77-80
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• 2003

The interaction of mastoparan B, a cationic tetradecapeptide amide isolated from the hornet Vespa basalis, with phospholipid bilayers was studied with synthetic mastoparan B and its analogue with Ala instead of hydrophobic 12th amino acid residue in mastoparan B. MP-B and its derivative, [12-Ala]MP-B were synthesized by the solid-phase peptide synthesis method. MP-B and its analogue, [12-Ala]MP-B adopted an unordered structure in buffer solution. In the presence of neutral and acidic liposomes, the peptides took an $\alpha$-helical structure. The two peptides interacted with neutral and acidic lipid bilayers. These results indicated that the hydrophobic face in the amphipathic $\alpha$-helix of MP-B critically affected the biological activity and helical content.

• 한국막학회:학술대회논문집
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• 한국막학회 1995년도 춘계 총회 및 학술발표회
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• pp.16-20
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• 1995

The spontaneous self-organization of amphiphilic molecules into complex aggregates was undoubtedly an important factor in the emergence of life on earth. We study the parameters governing the self-organization of a simple amphiphilic model system using electron cryomicroscopy of ice-embedded specimens in combination with extensive data analysis. Different stable helices can be generated reproducibly by changing the parameters controlling the molecular aggregation process. The repeating units of the helical aggregates in the micrographs can be found by multivariate statistical image analysis techniques, and these two-dimensional projection images suffice for calculating the three-dimensional density distribution of the fibers. We present a typical structure consisting of a narrow stack of compartmented bilayers twisted into a left-handed helix. Our new techniques directly elucidate the three-dimensional structure of helical assemblies, and can complement or replace diffraction-based approaches.

• Bulletin of the Korean Chemical Society
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• 제18권1호
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• pp.50-56
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• 1997

The mode of action of mastoparan B, an antimicrobial cationic tetradecapeptide amide isolated from the hornet Vespa basalis, toward phospholipid bilayers was studied with synthetic mastoparan B and its analogs with individual Ala instead of hydrophobic amino acids (1-Ile, 3-Leu, 6-Leu, 7-Val, 9-Trp, 13-Val, 14-Leu) in mastoparan B. Mastoparan B and its analogs were synthesized by the solid-phase method. Circular dichroism spectra showed that mastoparan B and its analogs adopted an unordered structure in buffer solution. In the presence of neutral and acidic liposomes, most of the peptides took an α-helical structure. The calcein leakage experiment indicated that mastoparan B interacted strongly with neutral and acidic lipid bilayers than its analogs. Mastoparan B also showed a more or less highly antimicrobial activity and hemolytic activity for human erythrocytes than its analogs. These results indicate that the hydrophobic face in the amphipathic α-helix of mastoparan B critically affect biological activity and helical contents.

• 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.

• Bulletin of the Korean Chemical Society
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• 제23권4호
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• pp.629-633
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• 2002

• 한국고분자학회지:고분자과학과기술
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• 제23권6호
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• pp.624-628
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• 2012

• 한국음향학회지
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• 제25권6호
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• pp.282-290
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• 2006

본 논문에서는 1.2 kbps 의 전송률을 가지는 초 저속 음성 부호화기를 위한 방법과 구조를 제안한다. ZFE-CELP (Zinc Function Excitation-Code Excited Linear Prediction) 음성 부호화기는 선형예측 분석 후, 추출된 잔여 신호가 유성음일 경우 Zinc Function을 이용하여 부호화하고, 무성음일 경우에는 CELP 구조를 이용하여 부호화한다. 또한 Super-frame (40ms) 의 영향으로 발생하는 하모닉의 불연속 문제를 해결하기 위해 오버 샘플링을 이용한 선형 위상 합성 기법을 이용하고 Zinc 함수의 정확한 표준파형을 추출하기 위하여 분석-합성 구조를 제안한다. 제안된 초 저속음성 부호화기의 성능을 2.4 kbps의 MELP (Multi Pulse Linear Prediction) 부호화기 및 1.9kbps의 ZFE-PWI (Zinc Function Excitation-Prototype Waveform Interpolation) 음성 부호화기와 비교하였다 제안된 부호화 방법은 19kbps ZFE-PWI 부호화기와 유사한 성능을 보이는 것을 확인하였다.

• Bulletin of the Korean Chemical Society
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• 제27권4호
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• pp.568-572
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• 2006

To study the effect of sequence on DNA structure, the two decamer crystal structures one alternating,d(GTACGCGTAC), and the other non-alternating, d(GGCCGCGGCC), were solved. Crystals of both decamers belong to the hexagonal space group $P6_122$, with one strand in the asymmetric unit. The unit cell constants of the alternating decamer are a = b = 39.26 $\AA$, c = 77.70 $\AA$. The structure was refined with 1,828 reflections from 8.0 to 2.0 Aresolution to an R value of 21.3% with all DNA atoms and 63 water molecules. The isomorphous non-alternating decamer had unit cell dimensions of a = b = 39.05 $\AA$, c = 82.15 $\AA$. The structure was refined with 2,423 reflections from 8.0 to 2.0 $\AA$ resolution to a final R value of 22.2% for all DNA atoms and 65 water molecules. Although the average helical parameters of the decamers are typical of A-DNAs, there are some minor differences between them. The helical twist, rise, x-displacement, inclination and roll alternate in the alternating decamer, but do not in the non-alternating decamer. The backbone conformations in both structures show some differences; the residue G(7) of the alternating decamer is trans for $\alpha$ and $\gamma$ while the trans conformations are observed at the residue G(8) of the non-alternating decamer.

• Bulletin of the Korean Chemical Society
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• 제25권1호
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• pp.63-68
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• 2004

Sugar-based gelator p-dodecanoyl-aminophenyl- ${\beta}$-D-aldopyranosides (1-3) have been shown to self-assemble in the presence of p-aminophenyl aldopyranosides. The hydrogel 1+4 showed the double-helical structure with 3-25 nm outer diameters, which is quite different from that of 1. The gel 2+5 revealed twisted ribbon structure with 30-50 nm in widths and a few micrometers of length whereas the gel 3+4 revealed the single and the bundled fiber structures. The difference in these gel supramolecular structures has successfully been transcribed into silica structures by sol-gel polymerization of tetraethoxysilane (TEOS), resulting in the doublehelical, the twisted-ribbon, the single and the multiple (lotus-shaped) hollow fiber structures. These results indicate that novel silica structures can be created by transcription of various superstructures formed in binary gels through the hydrogen-bonding interaction, and the amino group of the p-aminophenyl aldopyranosides acts as an efficient driving force to create novel silica nanotubes. Furthermore, electron energy-loss spectroscopy (ELLS) provided strong evidence for the inner hollow structure of the double-helical silica nanotube. This is a novel and successful example that a variety of new silica structures can be created using a library of carbohydrate gel fibers as their templates.

• Bulletin of the Korean Chemical Society
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• 제33권2호
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• pp.583-588
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• 2012

Functional interaction between Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product fushi tarazu (FTZ) is crucial for regulating genes related to define the identities of alternate segmental regions in the Drosophila embryo. FTZ binding to the ligand-binding domain (LBD) of FTZ-F1 is of essence in activating its transcription process. We determined solution structures of the cofactor peptide ($FTZ^{PEP}$) derived from FTZ by NMR spectroscopy. The cofactor peptide showed a nascent helical conformation in aqueous solution, however, the helicity was increased in the presence of TFE. Furthermore, $FTZ^{PEP}$ formed ${\alpha}$-helical conformation upon FTZ-F1 binding, which provides a receptor bound structure of $FTZ^{PEP}$. The solution structure of $FTZ^{PEP}$ in the presence of FTZ-F1 displays a long stretch of the ${\alpha}$-helix with a bend in the middle of helix.