• BMB Reports
• /
• 제42권3호
• /
• pp.160-165
• /
• 2009

The temperate Staphylococcus aureus phage ${\Phi}11$ harbors cI and cro repressor genes similar to those of lambdoid phages. Using extremely pure ${\Phi}11$ Cro (the product of the ${\Phi}11$ cro gene) we demonstrated that this protein possesses a single domain structure, forms dimers in solution at micromolar concentrations and maintains a largely $\alpha$-helical structure even at $45^{\circ}C$. ${\Phi}11$ Cro was sensitive to thermolysin at temperatures ranging from $55-75^{\circ}C$ and began to aggregate at ${\sim}63^{\circ}C$, suggesting that the protein is moderately thermostable. Of the three homologous 15-bp operators (O1, O2, and O3) in the ${\Phi}11$ cI-cro intergenic region, ${\Phi}11$ Cro only binds efficiently to O3, which is located upstream of the cI gene. Our comparative analyses indicate that the DNA binding capacity, secondary structure and dimerization efficiency of thermostable ${\Phi}11$ Cro are distinct from those of P22 Cro and $\lambda$ Cro, the best characterized representatives of the two structurally different Cro families.

• Nuclear Engineering and Technology
• /
• 제48권4호
• /
• pp.1022-1035
• /
• 2016

A double-tube once-through steam generator (DOTSG) consisting of an outer straight tube and an inner helical tube is studied in this work. First, the structure of the DOTSG is optimized by considering two different objective functions. The tube length and the total pressure drop are considered as the first and second objective functions, respectively. Because the DOTSG is divided into the subcooled, boiling, and superheated sections according to the different secondary fluid states, the pitches in the three sections are defined as the optimization variables. A multi-objective optimization model is established and solved by particle swarm optimization. The optimization pitch is small in the subcooled region and superheated region, and large in the boiling region. Considering the availability of the optimum structure at power levels below 100% full power, we propose a new operating scheme that can fix the boundaries between the three heat-transfer sections. The operation scheme is proposed on the basis of data for full power, and the operation parameters are calculated at low power level. The primary inlet and outlet temperatures, as well as flow rate and secondary outlet temperature are changed according to the operation procedure.

• Bulletin of the Korean Chemical Society
• /
• 제34권4호
• /
• pp.1120-1126
• /
• 2013

The syndecan family consists of four transmembrane heparan sulfate proteoglycans present in most cell types and each syndecan shares a common structure containing a heparan sulfate modified extracellular domain, a single transmembrane domain and a C-terminal cytoplasmic domain. To get a better understanding of the mechanism and function of syndecan-4 which is one of the syndecan family, it is crucial to investigate its three-dimensional structure. Unfortunately, it is difficult to prepare the peptide because it is membrane-bound protein that transverses the lipid bilayer of the cell membrane. Here, we optimize the expression, purification, and characterization of transmembrane, cytoplasmic and short extracellular domains of syndecan4 (syndecan-4 eTC). Syndecan-4 eTC was successfully obtained with high purity and yield from the M9 medium. The structural information of syndecan-4 eTC was investigated by MALDI-TOF mass (MS) spectrometry, circular dichroism (CD) spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. It was confirmed that syndecan-4 eTC had an ${\alpha}$-helical multimeric structure like transmembrane domain of syndecan-4 (syndecan-4 TM) in membrane environments.

• Journal of Microbiology and Biotechnology
• /
• 제16권9호
• /
• pp.1429-1433
• /
• 2006

Application of recombinant protein production and particularly their isotopic enrichment has stimulated development of a range of novel multidimensional heteronuclear NMR techniques. Peptides in most cases are amenable to assignment and structure determination without the need for isotopic labeling. However, there are many cases where the availability of $^{15}N$ and/or $^{13}C$ labeled peptides is useful to study the structure of peptides with more than 30 residues and the interaction between peptides and membrane. CRAMP (Cathelicidin-Related AntiMicrobial Peptide) was identified from a cDNA clone derived from mouse femoral marrow cells as a member of cathelicidin-derived antimicrobial peptides. CRAMP was successfully expressed as a GST-fused form in E. coli and purified using affinity chromatography and reverse-phase chromatography. The yield of the CRAMP was 1.5 mg/l 1. According to CD spectra, CRAMP adopted ${\alpha}$-helical conformation in membrane-mimetic environments. Isotope labeling of CRAMP is expected to make it possible to study the structure and dynamic properties of CRAMP in various membrane systems.

• 한국생물물리학회:학술대회논문집
• /
• 한국생물물리학회 2003년도 정기총회 및 학술발표회
• /
• pp.73-73
• /
• 2003

We report here the results on N-acetyl-N'-methylamide of alanine (Ac-Ala-NHMe) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-3l+G(d) basis set to investigate the conformational preference of alanine depending on the backbone torsion angles $\square$ and$\square$ in the gas phase, chloroform, and water. There are seven local minima (LM) in the gas phase and two additional LM are found in chloroform and water. These two additional LM A (an $\square$-helical structure) and F (a polyproline structure) are stabilized only in solutions. In the gas phase, the lowest LM is the conformation C with a C$\sub$7/ intramolecular hydrogen bond and the relative conformational energies range from 0.3 to 6.0 ㎉/mol. In chloroform, the lowest LM is the conformation E (an extended structure) and the relative conformational energies range from 0.7 to 4.9 ㎉/mol. In particular, we identified 14 possible transition states connecting between seven LM in the gas phase. The search for transition states probable in chloroform and water is now in progress.

• 천문학회보
• /
• 제36권1호
• /
• pp.35.2-35.2
• /
• 2011

We have investigated a coronal jet near the limb on 2010 June 27 by Hinode/X-Ray Telescope (XRT), EUV Imaging Spectrograph (EIS), SDO/Atmospheric Imaging Assembly (AIA), and STEREO. From EUV (AIA and EIS) and soft X-ray (XRT) images we identify the erupting jet feature in cool and hot temperatures. Using the high temporal and multi wavelength AIA images, we found that the hot jet preceded its associated cool jet and their structures are well consistent with the numerical simulation of the emerging flux-reconnection model. From the spectroscopic analysis, we found that the jet structure changes from blue shift to red one with time, which may indicate the helical structure of the jet. The STEREO observation, which enables us to observe this jet on the disk, shows that there was a dim loop associated with the jet. On the other hand, we found that the structure of its associated active region seen in STEREO is similar to that in AIA observed 5 days before. Based on this fact, we compared the jet morphology on the limb with the magnectic fields extrapolated from a HMI vector magnetogram of this active region observed on the disk. Interestingly, the comparison shows that the open and closed magnetic field configuration correspond to the jet and the dim loop, respectively, as the Shibata's jet model predicted.

• Bulletin of the Korean Chemical Society
• /
• 제19권1호
• /
• pp.57-62
• /
• 1998

We have synthesized a 17-residue peptide with the amino acid sequence RQMKEDAKGKSEEELAD corresponding to residues 84-100 of chicken skeletal troponin C. This stretch of the protein sequence is in the middle one-third of the 32-residue 9-turn α-helix that connects the two globular domains of the dumbell-shaped molecule and includes the D/E linker helix. We describe here the solution conformation of the helix linker as studied by circular dichroism (CD) and two-dimensional nuclear magnetic resonance (2-D NMR) spectroscopy. The NOE connectivities together with the vicinal $^3J_{N{\alpha}}$ coupling constants suggest that the peptide exists in a fast conformational equilibrium among several secondary structure: a nascent helix near the N-terminus, a helix, and a substational population of extended and random coil forms. In addition, two interresidue α-α NOEs are observed suggesting a bent structure with a bend that includes the single glycine in position 92. These results are consistent with the ideas that in neutral solution the D/E linker region of the central helix in troponin C can adopt a helical conformation and the central helix may have a segmental flexibility around Gly 92.

• Parasites, Hosts and Diseases
• /
• 제23권2호
• /
• pp.269-284
• /
• 1985

The metabolism of Entamoeba histolytica would be affected by various environmental factors, and alteration of the environment was known to afEect the fine structure of 5. histolytica. The present study was designed electronmicroscopically to investigate the ultrastructure and enzyme activities in the aEonic and conventional strains of 5. histolytica. The trophozoites of axenically cultivated HK-9 strain and conventional YS-27 and YS-49 strains of 5. histolytica were collected and liKed with 4% paraformaldehyde/0.1M cacodylate buffier(pH 74), After washing them by centrifugation, 1% warm agar was added in the sediment. Solidified agar with the trophozoites was cut into $lmm^3$ cubes, and incubated in the various substrates to observe enzyme activities. Then, the specimen was post-fixed with 3% glutaraldehyde/0.1M cacodylate buffer (PH 7.4) and 1% osmium tetroBide/0.1M cacodylate buffier (pH 7.4) , dehydrated in ascending ethanol series and embedded in epoxy resin. These were sectioned on an ultramicrotome and observed with a transmission electronmicroscope. The procedures for the observation of the fine structure were same as the above, except for the incubation in the substrate. The sections were stained with uranyl acetate and lead citrate. For the observation of the surface of the amoebae, scanning-electronmicroscopy was carried out. The results obtained in the present study are summarized as follows: 1. The fuzzy coat around double-layered plasma membrane of 5. histolytica was more irregularly and densely distributed in the conventional strains (YS-27, YS-49 strains) than in the axonic strain (HK-9 strain). 2. The endosomes, button bodies and chromatin material were surrounded by a double-layered nuclear membrane having scattered nuclear fores. The paranuclear body, mono- or double-layered vacuoles, vacuolar membrane whorls, rosette-like cylindrical bodies, aggregation of cylindrical bodies and helical bodies were found in the cytoplasm of the amoebae. Helical bodies and glycogen granules were generally abundant, while a few smooth endoplasmic reticula were observed in the cytoplasm. 3. Alkaline phosphatase activity was mainly demonstrated in the plasma membrane, limiting membranes of vacuoles and smooth endoplasmic reticula. ATPase activity was observed in the nucleus, limiting membranes of vacuoles and vacuolar membrane whorls. 4. Acid phosphatase activity was commonly demonstrated in the limiting membranes an contents of vacuoles, Iysosome-like organelles, plasma membrane and the button bodies in the nucleus. The activity was more weakly demonstrated in the HK-9 strain than in the other conventional strains of 5. histolytica. No peroBidase activity was observed in the amoeba strains employed in the present study. 5. With a scanning electron-microscope, no distinct structural differences were observed between the amoeba strains. All the trophozoite forms of the amoebae showed crater-like depressions and rugged features on the outer surface.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제31권1호
• /
• pp.14-19
• /
• 2015

In a previous report, we identified several candidate antimicrobial peptides through de novo RNA sequencing of the centipede Scolopendra subspinipes mutilans. Here, we identify and characterize one of these peptides, Scolopendrasin I. We identified the centipede antimicrobial peptide Cecropin from the centipede transcriptome using an SVM algorithm, and subsequently analyzed the amino acid sequence for predicted secondary structure using a GOR algorithm. We identified an alpha helical region of Cecropin and named it Scolopendrasin I. We then assessed antimicrobial and hemolytic activity of Scolopendrasin I. Scolopendrasin I showed antimicrobial activity against various microbes, including antibiotic-resistant Gram-negative bacteria, in a radial diffusion assay. Scolopendrasin I had potent antibacterial activity against acne-associated microbes in a colony count assay and showed no hemolytic activity in a hemolysis assay. In addition, we confirmed that Scolopendrasin I bound to the surface of bacteria via a specific interaction with lipoteichoic acid and lipopolysaccharide, two components of bacterial cell membranes. In conclusion, the results presented here provide evidence that this is an efficient strategy for antimicrobial peptide candidate identification and that Scolopendrasin I has potential for successful antibiotic development.

• BMB Reports
• /
• 제47권11호
• /
• pp.625-630
• /
• 2014

Defensins, which are small cationic molecules produced by organisms as part of their innate immune response, share a common structural scaffold that is stabilized by three disulfide bridges. Coprisin is a 43-amino acid defensin-like peptide from Copris tripartitus. Here, we report the intramolecular disulfide connectivity of cysteine-rich coprisin, and show that it is the same as in other insect defensins. The disulfide bond pairings of coprisin were determined by combining the enzymatic cleavage and mass analysis. We found that the loss of any single disulfide bond in coprisin eliminated all antibacterial, but not antifungal, activity. Circular dichroism (CD) analysis showed that two disulfide bonds, Cys20-Cys39 and Cys24-Cys41, stabilize coprisin's ${\alpha}$-helical region. Moreover, a BLAST search against UniProtKB database revealed that coprisin's ${\alpha}$-helical region is highly homologous to those of other insect defensins.