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Search Results: 1 - 10 of 14233 matches for " Tae-Ho Park "
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Purification, Crystallization and Preliminary X-ray Crystallographic Studies of RAIDD Death-Domain (DD)
Tae-ho Jang,Hyun Ho Park
International Journal of Molecular Sciences , 2009, DOI: 10.3390/ijms10062501
Abstract: Caspase-2 activation by formation of PIDDosome is critical for genotoxic stress induced apoptosis. PIDDosome is composed of three proteins, RAIDD, PIDD, and Caspase-2. RAIDD is an adaptor protein containing an N-terminal Caspase-Recruiting-Domain (CARD) and a C-terminal Death-Domain (DD). Its interactions with Caspase-2 and PIDD through CARD and DD respectively and formation of PIDDosome are important for the activation of Caspase-2. RAIDD DD cloned into pET26b vector was expressed in E. coli cells and purified by nickel affinity chromatography and gel filtration. Although it has been known that the most DDs are not soluble in physiological condition, RAIDD DD was soluble and interacts tightly with PIDD DD in physiological condition. The purified RAIDD DD alone has been crystallized. Crystals are trigonal and belong to space group P3121 (or its enantiomorph P3221) with unit-cell parameters a = 56.3, b = 56.3, c = 64.9 ? and γ = 120°. The crystals were obtained at room temperature and diffracted to 2.0 ? resolution.
Novel Disulfide Bond-Mediated Dimerization of the CARD Domain Was Revealed by the Crystal Structure of CARMA1 CARD
Tae-ho Jang, Jin Hee Park, Hyun Ho Park
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0079778
Abstract: CARMA1, BCL10 and MALT1 form a large molecular complex known as the CARMA1 signalosome during lymphocyte activation. Lymphocyte activation via the CARMA1 signalosome is critical to immune response and linked to many immune diseases. Despite the important role of the CARMA1 signalosome during lymphocyte activation and proliferation, limited structural information is available. Here, we report the dimeric structure of CARMA1 CARD at a resolution of 3.2 ?. Interestingly, although CARMA1 CARD has a canonical six helical-bundles structural fold similar to other CARDs, CARMA1 CARD shows the first homo-dimeric structure of CARD formed by a disulfide bond and reveals a possible biologically important homo-dimerization mechanism.
Scaling of Coulomb pseudo-potential in s-wave narrow-band superconductors
Tae-Ho Park,Han-Yong Choi
Physics , 2001, DOI: 10.1103/PhysRevB.65.052504
Abstract: The Coulomb pseudo-potential $\mu^*$ is extracted by fitting the numerically calculated transition temperature $T_c$ of the Eliashberg-Nambu equation which is extended to incorporate the narrow-band effects, that is, the vertex correction and the frequency dependence of the screened Coulomb interaction. It is shown that even for narrow-band superconductors, where the fermi energy $ \epsilon_F$ is comparable with the phonon frequency $ \omega_{ph}$, the Coulomb pseudo-potential is a pertinent parameter, and is still given by $\mu^* = \mu/[1+\mu \ln(\epsilon_F/\omega_{ph})] $, provided $\omega_{ph}$ is appropriately scaled.
Numerical renormalization group study of the symmetric Anderson-Holstein model: phonon and electron spectral functions
Gun Sang Jeon,Tae-Ho Park,Han-Yong Choi
Physics , 2002, DOI: 10.1103/PhysRevB.68.045106
Abstract: We study the symmetric Anderson-Holstein (AH) model at zero temperature with Wilson's numerical renormalization group (NRG) technique to study the interplay between the electron-electron and electron-phonon interactions. An improved method for calculating the phonon propagator using the NRG technique is presented, which turns out to be more accurate and reliable than the previous works in that it calculates the phonon renormalization explicitly and satisfies the boson sum rule better. The method is applied to calculate the renormalized phonon propagators along with the electron propagators as the onsite Coulomb repulsion $U$ and electron-phonon coupling constant $g$ are varied. As $g$ is increased, the phonon mode is successively renormalized, and for $g \gtrsim g_{co}$ crosses over to the regime where the mode splits into two components, one of which approaches back to the bare frequency and the other develops into a soft mode. The initial renormalization of the phonon mode, as $g$ is increased from 0, depends on $U$ and the hybridization $\Delta$; it gets softened (hardened) for $U \gtrsim (\lesssim) U_s (\Delta)$. Correlated with the emergence of the soft mode is the central peak of the electron spectral function severely suppressed. These NRG calculations will be compared with the standard Green's function results for the weak coupling regime to understand the phonon renormalization and soft mode.
Light-induced current in molecular junctions: Local field and non-Markov effects
Boris D. Fainberg,Maxim Sukharev,Tae-Ho Park,Michael Galperin
Physics , 2011, DOI: 10.1103/PhysRevB.83.205425
Abstract: We consider a two-level system coupled to contacts as a model for charge pump under external laser pulse. The model represents a charge-transfer molecule in a junction, and is a generalization of previously published results [B. D. Fainberg, M. Jouravlev, and A. Nitzan. Phys. Rev. B 76, 245329 (2007)]. Effects of local field for realistic junction geometry and non-Markov response of the molecule are taken into account within finite-difference time-domain (FDTD) and on-the-contour equation-of-motion (EOM) formulations, respectively. Our numerical simulations are compared to previously published results.
Dynamical mean-field theory of Hubbard-Holstein model at half-filling: Zero temperature metal-insulator and insulator-insulator transitions
Gun Sang Jeon,Tae-Ho Park,Jung Hoon Han,Hyun C. Lee,Han-Yong Choi
Physics , 2003, DOI: 10.1103/PhysRevB.70.125114
Abstract: We study the Hubbard-Holstein model, which includes both the electron-electron and electron-phonon interactions characterized by $U$ and $g$, respectively, employing the dynamical mean-field theory combined with Wilson's numerical renormalization group technique. A zero temperature phase diagram of metal-insulator and insulator-insulator transitions at half-filling is mapped out which exhibits the interplay between $U$ and $g$. As $U$ ($g$) is increased, a metal to Mott-Hubbard insulator (bipolaron insulator) transition occurs, and the two insulating states are distinct and can not be adiabatically connected. The nature of and transitions between the three states are discussed.
Quadruple 9-mer-based protein binding microarray with DsRed fusion protein
Min-Jeong Kim, Tae-Ho Lee, Yoon-Mok Pahk, Yul-Ho Kim, Hyang-Mi Park, Yang Choi, Baek Nahm, Yeon-Ki Kim
BMC Molecular Biology , 2009, DOI: 10.1186/1471-2199-10-91
Abstract: We facilitated the PBM technology using a DsRed fluorescent protein and a concatenated sequence of oligonucleotides. The PBM was designed in such a way that target probes were synthesized as quadruples of all possible 9-mer combinations, permitting unequivocal interpretation of the cis-acting elements. The complimentary DNA strands of the features were synthesized with a primer and DNA polymerase on microarray slides. Proteins were labeled via N-terminal fusion with DsRed fluorescent protein, which circumvents the need for a multi-step incubation. The PBM presented herein confirmed the well-known DNA binding sequences of Cbf1 and CBF1/DREB1B, and it was also applied to elucidate the unidentified cis-acting element of the OsNAC6 rice transcription factor.Our method demonstrated PBM can be conveniently performed by adopting: (1) quadruple 9-mers may increase protein-DNA binding interactions in the microarray, and (2) a one-step incubation shortens the wash and hybridization steps. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.Transcription factors (TFs) are regulatory proteins that interact with specific DNA sequences to control gene expression. The DNA binding domains of TFs bind to specific upstream sequences (cis-acting elements) of target genes and modulate the transcription process. Protein-DNA binding properties have been investigated by traditional procedures, such as the Electrophoretic Mobility Shift Assay (EMSA) and filter binding assay [1,2]. However, these methods are labor-intensive and are restricted to the intended application in that they are usually designed with prior knowledge obtained via promoter-reporter assays. Comprehensive genome-wide methods, along with the availability of whole-genome sequences and advances in microarray technology, have been developed to characterize protein-DNA binding specificities [3].Some of well-known high-throughput methods are chromatin immunoprecipitation
Far-Ultraviolet Observations of the Spica Nebula and the Interaction Zone
Yeon-Ju Choi,Kyoung-Wook Min,Kwang-Il Seon,Tae-Ho Lim,Young-Soo Jo,Jae-Woo Park
Physics , 2013, DOI: 10.1088/0004-637X/774/1/34
Abstract: We report the analysis results of far ultraviolet (FUV) observations, made for a broad region around $\alpha$ Vir (Spica) including the interaction zone of Loop I and the Local Bubble. The whole region was optically thin and a general correlation was seen between the FUV continuum intensity and the dust extinction, except in the neighborhood of the bright central star, indicating the dust scattering nature of the FUV continuum. We performed Monte-Carlo radiative transfer simulations to obtain the optical parameters related to the dust scattering as well as the geometrical structure of the region. The albedo and asymmetry factor were found to be 0.38$\pm$0.06 and 0.46$\pm$0.06, respectively, in good agreement with the Milky Way dust grain models. The distance to and the thickness of the interaction zone were estimated to be 70$^{+4}_{-8}$ pc and 40$^{+8}_{-10}$ pc, respectively. The diffuse FUV continuum in the northern region above Spica was mostly the result of scattering of the starlight from Spica, while that in the southern region was mainly due to the background stars. The \ion{C}{4} $\lambda\lambda$1548, 1551 emission was found throughout the whole region, in contrast to the \ion{Si}{2}* $\lambda$1532 emission which was bright only within the \ion{H}{2} region. This indicates that the \ion{C}{4} line arises mostly at the shell boundaries of the bubbles, with a larger portion likely from the Loop I than from the Local Bubble side, whereas the \ion{Si}{2}* line is from the photoionized Spica nebula.
FSTVAL: a new web tool to validate bulk flanking sequence tags
Joung Sug Kim, Jiye Kim, Tae-Ho Lee, Kyong Mi Jun, Tea Hoon Kim, Yul-Ho Kim, Hyang-Mi Park, Jong-Seong Jeon, Gynheung An, Ung-Han Yoon, Baek Hie Nahm, Yeon-Ki Kim
Plant Methods , 2012, DOI: 10.1186/1746-4811-8-19
Abstract: We present an open access web tool, flanking sequence tags validator (FSTVAL), to manage bulk flanking sequence tags (FSTs). FSTVAL automatically evaluates the FSTs and finds the best mapping positions of the FST against a known genome sequence. The statistics, in terms of genic and intergenic regions, are presented as a table, a distribution map, and a frequency graph along the chromosomes. Currently, 17 plant genome sequences, including Arabidopsis thaliana, Oryza sativa, and Glycine max, are available as reference genomes. We evaluated the utility and accuracy of the tool with 5,144 rice FSTs. The whole process, from uploading the sequences to generating tables of insertions, required a few minutes, with less than 4 clicks in the web environment.Run for 1?year and tested over 1,000 times, we have confirmed FSTVAL efficiently handles bulk FSTs. FSTVAL is freely available without login at http://bioinfo.mju.ac.kr/fstval/ webcite.
Significant association of SREBP-2 genetic polymorphisms with avascular necrosis in the Korean population
Tae-Ho Kim, Jeong-In Baek, Jung Hong, Su-Jin Choi, Hye-Jin Lee, Hyun-Ju Cho, Eui Park, Un-Kyung Kim, Shin-Yoon Kim
BMC Medical Genetics , 2008, DOI: 10.1186/1471-2350-9-94
Abstract: Four single nucleotide polymorphisms (SNP) in the SREBP-2 gene, IVS1+8408 T>C (rs2267439), IVS3-342 G>T (rs2269657), IVS11+414 G>A (rs1052717) and IVS12-1667 G>A (rs2267443), were selected from public databases and genotyped in 443 AVN patients and 273 control subjects by using single-based extension (SBE) genotyping.The minor allele (C) frequency of rs2267439 showed a significant protective effect on AVN (P = 0.01, OR; 0.75, 95% CI; 0.604–0.935), and the genotype frequencies of this polymorphism were also different from the controls in all alternative analysis models (P range, 0.009–0.03, OR; 0.647–0.744). In contrast, rs1052717 and rs2267443 polymorphisms were significantly associated with AVN risk. Further analysis based on pathological etiology showed that the genotypes of rs2267439, rs1052717 and rs2267443 were also significantly associated with AVN susceptibility in each subgroup.This study is the first report to evaluate the association between SREBP-2 gene polymorphisms and the susceptibility of AVN in the Korean population.Avascular necrosis (AVN), also known as osteonecrosis of the femoral head (ONFH), is a devastating bone disease that develops symptoms of articular destruction and bone collapse of the femoral head due to a disturbance in the supply of blood [1]. This disease mainly occurs in middle aged men, between 30 and 50 years of age. The pathogenic factor of AVN is not definite, but many previous studies have suggested that long term steroid usage [1-5] and alcohol abuse [6,7] are associated with AVN, and in some case it can also be idiopathic. These factors have a harmful influence on oxygen and nutrient supply to the bone through blood vessels in direct or indirect pathways. Steroid administration and alcohol abuse induce an increase of fatty vesicles in the circulation of the blood, causing fat embolism and increased lipid precipitation in osteocytes within the femoral head. Some previous experiments using animal models verified that alcohol fac
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