• Molecules and Cells
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• v.26 no.3
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• pp.228-235
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• 2008

Thiol-dependent redox systems are involved in regulation of diverse biological processes, such as response to stress, signal transduction, and protein folding. The thiol-based redox control is provided by mechanistically similar, but structurally distinct families of enzymes known as thiol oxidoreductases. Many such enzymes have been characterized, but identities and functions of the entire sets of thiol oxidoreductases in organisms are not known. Extreme sequence and structural divergence makes identification of these proteins difficult. Thiol oxidoreductases contain a redox-active cysteine residue, or its functional analog selenocysteine, in their active sites. Here, we describe computational methods for in silico prediction of thiol oxidoreductases in nucleotide and protein sequence databases and identification of their redox-active cysteines. We discuss different functional categories of cysteine residues, describe methods for discrimination between catalytic and noncatalytic and between redox and non-redox cysteine residues and highlight unique properties of the redox-active cysteines based on evolutionary conservation, secondary and three-dimensional structures, and sporadic replacement of cysteines with catalytically superior selenocysteine residues.

• Journal of Powder Materials
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• v.7 no.1
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• pp.12-18
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• 2000

Effects of the microstrucrure of rapidy solidified Al-Pb-Cu-Mg alloys on the wear investigated. In order to overcome the miscility gap between Al and pb under equilibrium conditions, both in the solid and the liquid states, the alloy were rapidy solidifies to produce them in a segregation-free condition. Although the Pb particles showed relatively fine dispersion in the Al matrix in all the alloys by this process. the Al-16Pb alloy was found to have the most favorable microstructure with discretre with discrete Pb particles of abount 0.5 ${\mu}$m in size. With the addition of Cu and Cu-Mg to Al-16Pb, cellular structures were newly formed; not seen in the binary Al-Pb alloy. Wear properties of the Al-Pb binary alloys measured as a function of the sliding speen, sliding distance, and applied load showed that the Al-16Pb alloy has the best wear resistance, as expected from the fine microstructural features in this alloy. The were resistance of the alloy containing Cu-and Cu-Mg was higher than that of the Al-16Pvb alloy, due to matrix strengthening by precipitation hardeing. The wear mechanism was identified by examining the traces and wear debris.

• Journal of Korea Foundry Society
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• v.15 no.5
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• pp.459-468
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• 1995

For high performance aerospace structures, the properties of highest priority are low density, high strength, and high stiffness(modulus of elasticity). Addition of beryllium decrease the density of the aluminum alloy and increase the strength and the stiffness of the alloy. However it is very difficult to produce the Al-Be alloy having useful engineering properties by conventional ingot casting, because of the extremely limited solid solubility of beryllium in aluminum. So, rapid solidification processing is necessary to obtain extended solid solubility. In this study, rapidly solidified Al-6 at% Be alloy were prepared by twin roll melt spinning process and single roll melt spinning process. Twin roll melt spun ribbons were extruded at $450^{\circ}C$ with reduction in area of 25 : 1 after vacuum hot pressing at $550^{\circ}C and 375^{\circ}C$. The microstructure of melt spun ribbon exhibited a refined cellular microstructure with dispersed Be particles. As advance velocity of liquid/solid interface increase, the morphology of Be particle vary from rod-like type to spherical type and the crystal structure of Be particle from HCP to BCC. These microstructural characteristics of rapidly solidified Al-6at.%Be alloy were described on the basis of metastable phase diagram proposed by Perepezko and Boettinger. The extruded ribbon consisted of recrystallized grains dispersed with Be particles and exhibited improved tensile property compared with that of extruded ingot.

• Molecules and Cells
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• v.25 no.3
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• pp.352-357
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• 2008

Osteoprotegerin (OPG) is a soluble decoy receptor that inhibits osteoclastogenesis and is closely associated with bone resorption processes. We have designed and determined the solution structures of potent OPG analogue peptides, derived from sequences of the cysteine-rich domain of OPG. The inhibitory effects of the peptides on osteoclastogenesis are dose-dependent ($10^{-6}M-10^{-4}M$), and the activity of the linear peptide at $10^{-4}M$ is ten-fold higher than that of the cyclic OPG peptide. Both linear and cyclic peptides have a ${\beta}$-turn-like conformation and the cyclic peptide has a rigid conformation, suggesting that structural flexibility is an important factor for receptor binding. Based on structural and biochemical information about RANKL and the OPG peptides, we suggest that complex formation between the peptide and RANKL is mediated by both hydrophobic and hydrogen bonding interactions. These results provide structural insights that should aid in the design of peptidyl-mimetic inhibitors for treating metabolic bone diseases caused by abnormal osteoclast recruitment.

• Journal of Microbiology and Biotechnology
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• v.16 no.9
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• pp.1453-1458
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• 2006

PKR-like endoplasmic reticulum (ER) kinase (PERK) is a type I transmembrane ER-resident protein containing a cytoplasmic catalytic domain with a Ser/Thr kinase activity, which is most closely related to the eukaryotic translation initiation factor-$2{\alpha}$ ($eIF2{\alpha}$) kinase PKR involved in the antiviral defense pathway by interferon. We cloned and expressed the PERK C-terminal kinase domain (cPERK) in Escherichia coli. Like PERK activation in cells under ER stress, wild-type cPERK underwent autophosphorylation when overexpressed in E. coli, whereas the cPERK(K621M) with a methionine substitution for the lysine at amino acid 621 lost the autophosphorylation activity. The activated form cPERK which was purified to near homogeneity, formed an oligomer and was able to trans-phosphorylate specifically its cellular substrate $eIF2{\alpha}$. Two-dimensional phosphoamino acids analysis revealed that phosphorylation of cPERK occurs at the Ser and Thr residues. The functionally active recombinant cPERK, and its inactive mutant should be useful for the analysis of biochemical functions of PERK and for the determination of their three-dimensional structures.

• Wind and Structures
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• v.23 no.1
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• pp.19-43
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• 2016

In the present study, a new methodology is presented to study the ride comfort and bridge responses of a long-span bridge-traffic-wind coupled vibration system considering stochastic characteristics of traffic flow and bridge surface progressive deterioration. A three-dimensional vehicle model with 24 degrees-of-freedoms (DOFs) including a three-dimensional non-linear suspension seat model and the longitudinal vibration of the vehicle is firstly presented to study the ride comfort. An improved cellular automaton (CA) model considering the influence of the next-nearest neighbor vehicles and a progressive deterioration model for bridge surface roughness are firstly introduced. Based on the equivalent dynamic vehicle model approach, the bridge-traffic-wind coupled equations are established by combining the equations of motion of both the bridge and vehicles in traffic using the displacement relationship and interaction force relationship at the patch contact. The numerical simulations show that the proposed method can simulate rationally the ride comfort and bridge responses of the bridge-traffic-wind coupled system; and the vertical, lateral, and longitudinal vibrations of the driver seat model can affect significantly the driver's comfort, as expected.

• Wind and Structures
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• v.24 no.3
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• pp.287-306
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• 2017

In the present study, a new assessment simulation of ride safety based on a new wind-traffic-pavement-bridge coupled vibration system is developed considering stochastic characteristics of traffic flow and bridge surface. Compared to existing simulation models, the new assessment simulation focuses on introducing the more realistic three-dimensional vehicle model, stochastic characteristics of traffic, vehicle accident criteria, and bridge surface conditions. A three-dimensional vehicle model with 24 degrees-of-freedoms (DOFs) is presented. A cellular automaton (CA) model and the surface roughness are introduced. The bridge deck pavement is modeled as a boundless Euler-Bernoulli beam supported on the Kelvin model. The wind-traffic-pavement-bridge coupled equations are established by combining the equations of both the vehicles in traffic, pavement, and bridge using the displacement and interaction force relationship at the patch contact. The numerical simulation shows that the proposed method can simulate rationally useful assessment and prevention information for traffic, and define appropriate safe driving speed limits for vulnerable vehicles under normal traffic and bridge surface conditions.

• The Korean Journal of Zoology
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• v.13 no.4
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• pp.112-126
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• 1970

This paper deals with cytogenetical and cytochemical studies of the carp (Cyprinus carpio), the funa (Carassius carassius) and their hybrids. When kept under a confined condition, the carp and the funa mate andcan produce hybrids. Reciprocal crosses are also possible with similar results. The hybrids grow regularly with no observed abnormalities in the course of their development. They rank intermediate between the parent species in several characters. The hybrid males are completely sterile, while a hybrid female laid eggs in backcrossing. The spermatogenetic activity in hybrid testes is greatly disturbed. The chromosomes as observed in spermatogonial devision of hybrids are 100 in number, being the total sum of the haploid numbers of the parents, 50 for the carp and 50 for the funa. Meiosis in the hybrid testes is highly disturbed being arrested at early stages of the meiotic prophase. Most of the germ-cells undergo pycnotic degeneration during the period from late leptotene, and no spermatozoa are produced. In some hybrid specimens, the gonads show mosaic structures composed of testicular and ovarian elements, anevidence suggesting that sterility is associated with intersexuality caused by genetic unbalance between the parent species. The DNA amount in spermatogonial nuclei of thehybrids is approximately the same as that of liver nuclei, showing the 2n value. The DNA amount in the pachytene nuclei of the hybrids is less than the 4n value, while the parent species have the reduced amount of DNA in their pachytene nuclei. A consideration was made that the reduced amount of DNA in the hybrid cells may cause the disturbance of cellular activity leading to the subsequent degeneration of cells. Some aspects of enzymatic pattern in the carp, funa and their hybrids are. going on.

• Molecules and Cells
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• v.38 no.2
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• pp.171-179
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• 2015

Prostatic acid phosphatase (PAP) expression increases proportionally with prostate cancer progression, making it useful in prognosticating intermediate to high-risk prostate cancers. A novel ligand that can specifically bind to PAP would be very helpful for guiding prostate cancer therapy. RNA aptamers bind to target molecules with high specificity and have key advantages such as low immunogenicity and easy synthesis. Here, human PAP-specific aptamers were screened from a 2'-fluoropyrimidine (FY)-modified RNA library by SELEX. The candidate aptamer families were identified within six rounds followed by analysis of their sequences and PAP-specific binding. A gel shift assay was used to identify PAP binding aptamers and the 6N aptamer specifically bound to PAP with a Kd value of 118 nM. RT-PCR and fluorescence labeling analyses revealed that the 6N aptamer bound to PAP-positive mammalian cells, such as PC-3 and LNCaP. IMR-90 negative control cells did not bind the 6N aptamer. Systematic minimization analyses revealed that 50 nucleotide sequences and their two hairpin structures in the 6N 2'-FY RNA aptamer were equally important for PAP binding. Renewed interest in PAP combined with the versatility of RNA aptamers, including conjugation of anti-cancer drugs and nano-imaging probes, could open up a new route for early theragnosis of prostate cancer.

• Molecules and Cells
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• v.43 no.9
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• pp.804-812
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• 2020

In cells, proteins form macromolecular complexes to execute their own unique roles in biological processes. Conventional structural biology methods adopt a bottom-up approach starting from defined sets of proteins to investigate the structures and interactions of protein complexes. However, this approach does not reflect the diverse and complex landscape of endogenous molecular architectures. Here, we introduce a top-down approach called Electron Microscopy screening for endogenous Protein ArchitectureS (EMPAS) to investigate the diverse and complex landscape of endogenous macromolecular architectures in an unbiased manner. By applying EMPAS, we discovered a spiral architecture and identified it as AdhE. Furthermore, we performed screening to examine endogenous molecular architectures of human embryonic stem cells (hESCs), mouse brains, cyanobacteria and plant leaves, revealing their diverse repertoires of molecular architectures. This study suggests that EMPAS may serve as a tool to investigate the molecular architectures of endogenous macromolecular proteins.