• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2203-2208
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• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.

• Journal of the Korean Chemical Society
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• v.54 no.4
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• pp.387-394
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• 2010

The theoretical calculations for $B_nH_n$, $B_nH_{n+1}$, $B_nH_{n+2}$ (n = 3-6) have been considered at the B3LYP level of theory with the 6-311G$^*$ basis set. The optimized geometries, harmonic vibrational frequencies, and binding energies are evaluated to elucidate the thermodynamic stability and spectroscopic properties. The harmonic vibrational frequencies for the molecules considered in this study show all real numbers implying true minima and the binding energies are corrected using zero-point vibrational energies (ZPVE). The binding energies and average energies due to increasing of BH monomer are predicted.

• Animal cells and systems
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• v.16 no.2
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• pp.87-94
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• 2012

Nur77 is a member of the nuclear receptor 4A (NR4A) subgroup, which has been implicated in energy metabolism. Although Nur77 is found in adipose tissue, where TR4 plays a key role in lipid homeostasis, the role of Nur77 in adipogenesis is still controversial. Although the Nur77 responsive element (AAAGGTCA) is partially overlapped with TR4-binding sites (AGGTCA $n$ AGGTCA: $n$=0-6), the regulatory role of Nur77 in TR4 function associated with adipocyte biology remains unclear. Here, we found that Nur77 inhibits adipogenesis and TR4 transcriptional activity. Treatment with a Nur77 agonist, 1,1-bis(3'-indolyl)-1-($p$-anisyl)-methane, during 3T3-L1 adipocyte differentiation reduced adipogenesis. In reporter gene analysis, Nur77 specifically suppressed TR4 transcription activity but had little effect on $PPAR{\gamma}$ transcription activity. Consistently, Nur77 also suppressed TR4-induced promoter activity of the TR4 target gene PEPCK, which is known to be important for glyceroneogenesis in adipose tissue. Furthermore, Nur77 suppressed TR4 binding to TR4 response elements without direct interaction with TR4, suggesting that Nur77 may inhibit TR4 transcription activity via binding competition for TR4-binding sites. Furthermore, DIM-C-$pPhOCH_3$ substantially suppressed TR4-induced PEPCK expression in 3T3-L1 adipocytes. Together, our data demonstrate that Nur77 plays an inhibitory role in TR4-induced PEPCK expression in 3T3-L1 adipocytes.

• Bulletin of the Korean Chemical Society
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• v.33 no.6
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• pp.1839-1844
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• 2012

We have investigated binding between wild-type and mutant Heat Shock Factor (HSF) DNA binding domains (DBDs) with 17-bp HSE containing a central 5'-NGAAN-3' element by equilibrium analytical ultracentrifugation using multi-wavelength technique. Our results indicate that R102 plays critical role in HSE recognition and the interactions are characterized by substantial negative changes of enthalpy (${\Delta}H^0_{\theta}=-9.90{\pm}1.13kcal\;mol^{-1}$) and entropy (${\Delta}S^0_{\theta}=-12.46{\pm}3.77cal\;mol^{-1}K^{-1}$) with free energy change, ${\Delta}G^0_{\theta}$ of $-6.15{\pm}0.03kcal\;mol^{-1}$. N105 plays minor role in the HSE interactions with ${\Delta}H^0_{\theta}$ of $-2.54{\pm}1.65kcal\;mol^{-1}$, ${\Delta}S^0_{\theta}$ of $19.28{\pm}5.50cal\;mol^{-1}K^{-1}$ and ${\Delta}G^0_{\theta}$ of $-8.35{\pm}0.05kcal\;mol^{-1}$, which are similar to those observed for wild-type DBD:HSE interactions (${\Delta}H^0_{\theta}=-3.31{\pm}1.86kcal\;mol^{-1}$, ${\Delta}S^0_{\theta}=17.38{\pm}6.20cal\;mol^{-1}K^{-1}$ and ${\Delta}G^0_{\theta}=-8.55{\pm}0.06kcal\;mol^{-1}$) indicating higher entropy contribution for both wild-type and N105A DBD bindings to the HSE.

• Journal of Microbiology and Biotechnology
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• v.26 no.6
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• pp.1077-1086
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• 2016

Glycerol dehydrogenases (GlyDHs) are essential for glycerol metabolism in vivo, catalyzing its reversible reduction to 1,3-dihydroxypropranone (DHA). The gldA gene encoding a putative GlyDH was cloned from Thermoanaerobacterium thermosaccharolyticum DSM 571 (TtGlyDH) and expressed in Escherichia coli. The presence of Mn²⁺ enhanced its enzymatic activity by 79.5%. Three highly conserved residues (Asp¹⁷¹, His²⁵⁴, and His²⁷¹) in TtGlyDH were associated with metal ion binding. Based on an investigation of glycerol oxidation and DHA reduction, TtGlyDH showed maximum activity towards glycerol at 60℃ and pH 8.0 and towards DHA at 60℃ and pH 6.0. DHA reduction was the dominant reaction, with a lower K_m(DHA) of 1.08 ± 0.13 mM and V_max of 0.0053 ± 0.0001 mM/s, compared with glycerol oxidation, with a K_m(glycerol) of 30.29 ± 3.42 mM and V_max of 0.042 ± 0.002 mM/s. TtGlyDH had an apparent activation energy of 312.94 kJ/mol. The recombinant TtGlyDH was thermostable, maintaining 65% of its activity after a 2-h incubation at 60℃. Molecular modeling and site-directed mutagenesis analyses demonstrated that TtGlyDH had an atypical dinucleotide binding motif (GGG motif) and a basic residue Arg⁴³, both related to dinucleotide binding.

• Genomics & Informatics
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• v.19 no.3
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• pp.29.1-29.10
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• 2021

In our previous studies, we have demonstrated the association of certain variants of the thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), and thyroglobulin (TG) genes with congenital hypothyroidism. Herein, we explored the mechanistic basis for this association using different in silico tools. The mRNA 3'-untranslated region (3'-UTR) plays key roles in gene expression at the post-transcriptional level. In TSHR variants (rs2268477, rs7144481, and rs17630128), the binding affinity of microRNAs (miRs) (hsa-miR-154-5p, hsa-miR-376a-2-5p, hsa-miR-3935, hsa-miR-4280, and hsa-miR-6858-3p) to the 3'-UTR is disrupted, affecting post-transcriptional gene regulation. TPO and TG are the two key proteins necessary for the biosynthesis of thyroid hormones in the presence of iodide and H₂O₂. Reduced stability of these proteins leads to aberrant biosynthesis of thyroid hormones. Compared to the wild-type TPO protein, the p.S398T variant was found to exhibit less stability and significant rearrangements of intra-atomic bonds affecting the stoichiometry and substrate binding (binding energies, ΔG of wild-type vs. mutant: -15 vs. -13.8 kcal/mol; and dissociation constant, K_d of wild-type vs. mutant: 7.2E^-12 vs. 7.0E^-11 M). The missense mutations p.G653D and p.R1999W on the TG protein showed altered ΔG(0.24 kcal/mol and 0.79 kcal/mol, respectively). In conclusion, an in silico analysis of TSHR genetic variants in the 3'-UTR showed that they alter the binding affinities of different miRs. The TPO protein structure and mutant protein complex (p.S398T) are less stable, with potentially deleterious effects. A structural and energy analysis showed that TG mutations (p.G653D and p.R1999W) reduce the stability of the TG protein and affect its structure-functional relationship.

• Journal of Veterinary Science
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• v.22 no.1
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• pp.12.1-12.11
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• 2021

Background: Bats have been considered natural reservoirs for several pathogenic human coronaviruses (CoVs) in the last two decades. Recently, a bat CoV was detected in the Republic of Korea; its entire genome was sequenced and reported to be genetically similar to that of the severe acute respiratory syndrome CoV (SARS-CoV). Objectives: The objective of this study was to compare the genetic sequences of SARS-CoV, SARS-CoV-2, and the two Korean bat CoV strains 16BO133 and B15-21, to estimate the likelihood of an interaction between the Korean bat CoVs and the human angiotensin-converting enzyme 2 (ACE2) receptor. Methods: The phylogenetic analysis was conducted with the maximum-likelihood (ML) method using MEGA 7 software. The Korean bat CoVs receptor binding domain (RBD) of the spike protein was analyzed by comparative homology modeling using the SWISS-MODEL server. The binding energies of the complexes were calculated using PRODIGY and MM/GBGA. Results: Phylogenetic analyses of the entire RNA-dependent RNA polymerase, spike regions, and the complete genome revealed that the Korean CoVs, along with SARS-CoV and SARS-CoV-2, belong to the subgenus Sarbecovirus, within BetaCoVs. However, the two Korean CoVs were distinct from SARS-CoV-2. Specifically, the spike gene of the Korean CoVs, which is involved in host infection, differed from that of SARS-CoV-2, showing only 66.8%-67.0% nucleotide homology and presented deletions within the RBD, particularly within regions critical for cross-species transmission and that mediate interaction with ACE2. Binding free energy calculation revealed that the binding affinity of Korean bat CoV RBD to hACE2 was drastically lower than that of SARS-CoV and SARS-CoV-2. Conclusions: These results suggest that Korean bat CoVs are unlikely to bind to the human ACE2 receptor.

• Advances in nano research
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• v.12 no.2
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• pp.213-221
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• 2022

Silicon carbide (SiC) is a binary carbon-silicon compound. In its two-dimensional form, monolayer SiC is composed of a monolayer carbon and silicon atoms constructed as a honeycomb lattice. SiC has recently been receiving increasing attention from researchers owing to its intriguing electronic properties. In this present work, SiC nanoribbons (SiCNRs) are modelled and simulated to obtain accurate electronic properties, which can further guide fabrication processes, through bandgap engineering. The primary objective of this work is to obtain the electronic properties of monolayer SiCNRs by applying numerical computation methods using nearest-neighbour tight-binding models. Hamiltonian operator discretization and approximation of plane wave are assumed for the models and simulation by applying the basis function. The computed electronic properties include the band structures and density of states of monolayer SiCNRs of varying width. Furthermore, the properties are compared with those of graphene nanoribbons. The bandgap of ASiCNR as a function of width are also benchmarked with published DFT-GW and DFT-GGA data. Our nearest neighbour tight-binding (NNTB) model predicted data closer to the calculations based on the standard DFT-GGA and underestimated the bandgap values projected from DFT-GW, which takes in account the exchange-correlation energy of many-body effects.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.8
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• pp.1180-1185
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• 2009

Two experiments were carried out to study the effects of dietary energy level on nutrient digestion, nitrogen (N) utilization, growth performance, insulin-like growth factor-I (IGF-I), and insulin-like growth factor binding protein-3 (IGFBP-3) in plasma, liver and longissimus dorsi muscle in growing-finishing pigs. In experiment 1 (Exp 1), 15 castrated male pigs (Duroc${\times}$Landrace${\times}$Large White) (Body weight, BW, 55.6${\pm}$1.8 kg) were divided into three groups and fed rations containing 13.33, 14.87 and 17.35 MJ digestible energy (DE)/kg as treatments I, II and III, respectively, using soybean oil as an energy source. The experiment lasted 8 days and faecal and urinary samples were collected during the last 3 days. The results showed that the digestibility of dry matter (DM), energy and N was increased from treatments I to III (p<0.01). N-retention and N-retention rate were not influenced by dietary DE level (p>0.05). In experiment 2 (Exp 2), 36 female pigs (Duroc${\times}$Landrace${\times}$Large White) (BW 41.5${\pm}$3.8 kg) were divided into three groups. The pigs were fed with the same three rations used in Exp 1 for 60 days. At the end of Exp 2, eight pigs were selected from each group for blood sampling and 4 pigs for slaughter trial. The results indicated that average daily feed intake (ADFI) and N-intake were significantly decreased (p<0.01), and DE intake (p<0.01) and average daily gain (ADG) (p<0.05) were increased. IGF-I and IGFBP-3 in plasma were increased (p<0.05). No significant differences in IGF-I and IGFBP-3 in liver and longissimus dorsi muscle were found between different treatments. It was concluded that higher dietary DE level improved nutrient digestibility, ADG and feed/gain ratio when soybean oil was used as an energy source in the ration of growing-finishing pigs. No significant differences were found in Nretention and IGF-I and IGFBP-3 in liver and longissimus dorsi muscle between different treatments.

• Journal of the Korean Vacuum Society
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• v.5 no.4
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• pp.315-326
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• 1996

The electronic structures of 3d and 4d core-levels of rare-earth atoms in the insulating rare-earth (Sm, Eu, Gd, and Tb) compounds were studied with x-ray photoelectron spectroscopy(XPS). It is shown that the intrinsic satellite structure due to the hybridization disappears for chemically stable-earth trivalent heavy rare-earth insulating compounds as the hybridization between f electrons of rare-earth atoms and p electrons of anion atoms decreases due to the lanthanide contraction. Eu atoms at the surface of the stable insulating trivalent Eu compounds are found to be divalent. The satellite peak of Eu 3d core-level spectra at about 10eV higher binding energy side relative the main peak comes from the multiplet structures of $\underline{3d}4f^6$ configuration. The satellite structure appearing at about 15 eV higher binding energy side relative to the main peak in all insulating rare-earth compounds is due to an energy loss process of creating a plasmon.