• Journal of Korean Society for Atmospheric Environment
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• v.31 no.4
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• pp.368-377
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• 2015

Bunker C fuel oil is a high-viscosity oil obtained from petroleum distillation as a residue. The sulfur content of bunker C fuel oil is limited to 4.0% or even lower to protect the environment. Because bunker C fuel oil is burned in a furnace or boiler for the generation of heat or used in an engine for the generation of power, carbon dioxide is emitted as a result of combustion. The objective of this study is to investigate $CO_2$ emission characteristics of bunker C fuel oil by sulfur contents. Calorific values and carbon contents of the fuels were measured using the oxygen bomb calorimeter method and the CHN elemental analysis method, respectively. Sulfur and hydrogen contents, which were used to calculate the net calorific value, were also measured and then net calorific values and $CO_2$ emission factors were determined. The results showed that hydrogen content increases and carbon content decreases by reducing sulfur contents for bunker C fuel oil with sulfur contents less than 1.0%. For sulfur contents between 1.0% and 4.0%, carbon content increases as sulfur content decreases but there is no evident variation in hydrogen content. Net calorific value increases by reducing sulfur contents. $CO_2$ emission factor, which is calculated by dividing carbon content by net calorific value, decreases as sulfur content decreases for bunker C fuel oil with sulfur contents less than 1.0% but it showed relatively constant values for sulfur contents between 1.0% and 4.0%.

• Journal of Energy Engineering
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• v.17 no.1
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• pp.15-22
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• 2008

This study was carried out to investigate physical and chemical characteristics of the distillates and residue of Athabasca oilsand bitumen obtained from Canada, using a vacuum distillation unit. The distillates and residue produced from the vacuum distillation were characterized through atomic analysis, SARA analysis, and measurement of boiling point distribution, molecular weight, and API gravity. The vacuum distillation equipment consisted of a 6-litter volume vessel, a glass-packed column, a condenser, a reflux device, a flask fer collecting distillates, and a temperature controller. The cutting of distillates was performed with four steps under the condition of full vacuum and maximum temperature of $320^{\circ}C$. The results showed that the sulfur amount and average molecular weight of the distillates were significantly reduced compared to those of oilsand bitumen. As the cutting temperature increased, the hydrogen amount decreased but the sulfur amount and average molecular weight increased in the distillates.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2497-2502
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• 2010

Arg13 is a conserved active-site residue in all known Pi class glutathione S-transferases (GSTs) and in most Alpha class GSTs. To evaluate its contribution to substrate binding and catalysis of this residue, three mutants (R13A, R13K, and R13L) were expressed in Escherichia coli and purified by GSH affinity chromatography. The substitutions of Arg13 significantly affected GSH-conjugation activity, while scarcely affecting glutathione peroxidase or steroid isomerase activities. Mutation of Arg13 into Ala largely reduced the GSH-conjugation activity by approximately 85 - 95%, whereas substitutions by Lys and Leu barely affected activity. These results suggest that, in the GSH-conjugation activity of hGST P1-1, the contribution of Arg13 toward catalytic activity is highly dependent on substrate specificities and the size of the side chain at position 13. From the kinetic parameters, introduction of larger side chains at position 13 results in stronger affinity (Leu > Lys, Arg > Ala) towards GSH. The substitutions of Arg13 with alanine and leucine significantly affected $k_{cat}$, whereas substitution with Lys was similar to that of the wild type, indicating the significance of a positively charged residue at position 13. From the plots of log ($k_{cat}/{K_m}^{CDNB}$) against pH, the $pK_a$ values of the thiol group of GSH bound in R13A, R13K, and R13L were estimated to be 1.8, 1.4, and 1.8 pK units higher than the $pK_a$ value of the wild-type enzyme, demonstrating the contribution of the Arg13 guanidinium group to the electrostatic field in the active site. From these results, we suggest that contribution of Arg13 in substrate binding is highly dependent on the nature of the electrophilic substrates, while in the catalytic mechanism, it stabilizes the GSH thiolate through hydrogen bonding.

• Molecules and Cells
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• v.38 no.5
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• pp.409-415
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• 2015

Low-barrier hydrogen bonds (LBHBs) have been proposed to have important influences on the enormous reaction rate increases achieved by many enzymes. ${\Delta}^5$-3-ketosteroi isomerase (KSI) catalyzes the allylic isomerization of ${\Delta}^5$-3-ketosteroid to its conjugated ${\Delta}^4$-isomers at a rate that approache the diffusion limit. Tyr14, a catalytic residue of KSI, has been hypothesized to form an LBHB with the oxyanion of a dienolate steroid intermediate generated during the catalysis. The unusual chemical shift of a proton at 16.8 ppm in the nuclear magnetic resonance spectrum has been attributed to an LBHB between Tyr14 $O{\eta}$ and C3-O of equilenin an intermediate analogue, in the active site of D38N KSI. This shift in the spectrum was not observed in Y30F/Y55F/D38N and Y30F/Y55F/Y115F/D38N mutant KSIs when each mutant was complexed with equilenin, suggesting that Tyr14 could not form LBHB with the intermediate analogue in these mutant KSIs. The crystal structure of Y30F/Y55F/Y115F/D38N-equilenin complex revealed that the distance between Tyr14 $O{\eta}$ and C3-O of the bound steroi was within a direct hydrogen bond. The conversion of LBHB to an ordinary hydrogen bond in the mutant KSI reduced the binding affinity for the steroid inhibitors by a factor of 8.1-11. In addition, the absence of LBHB reduced the catalytic activity by only a factor of 1.7-2. These results suggest that the amount of stabilization energy of the reaction intermediate provided by LBHB is small compared with that provided by an ordinary hydrogen bond in KSI.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.17-25
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• 2003

Determining the binding sites in protein-nucleic acid complexes is essential to the complete understanding of protein-nucleic acid interactions and to the development of new drugs. We have developed a set of algorithms for analyzing protein-nucleic acid interactions and for predicting potential binding sites in protein-nucleic acid complexes. The algorithms were used to analyze the hydrogen-bonding interactions in protein-RNA and protein-DNA complexes. The analysis was done both at the atomic and residue level, and discovered several interesting interaction patterns and differences between the two types of nucleic acids. The interaction patterns were used for predicting potential binding sites in new protein-RNA complexes.

• BMB Reports
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• v.39 no.2
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• pp.223-227
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• 2006

Dihydrolipoamide dehydrogenase (E3) belongs to the pyridine nucleotide-disulfide oxidoreductase family including glutathione reductase and thioredoxin reductase. It catalyzes the reoxidation of dihydrolipoyl moiety of the acyltransferase components of three $\alpha$-keto acid dehydrogenase complexes and of the hydrogen-carrier protein of the glycine cleavage system. Isoleucine-51 of human E3, located near the active disulfide center Cys residues, is highly conserved in most E3s from several sources. To examine the importance of this highly conserved Ile-51 in human E3 function, it was substituted with Ala using site-directed mutagenesis. The mutant was expressed in Escherichia coli and highly purified using an affinity column. Its E3 activity was decreased about 100-fold, indicating that the conservation of the Ile-51 residue in human E3 was very important to the efficient catalytic function of the enzyme. Its altered spectroscopic properties implied that conformational changes could occur in the mutant.

• Bulletin of the Korean Chemical Society
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• v.35 no.7
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• pp.2123-2129
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• 2014

Pim kinases are promising targets in the treatment of hematopoietic and solid cancers. Meridianin C was chosen as a starting point to discover novel pim kinase inhibitors. Using known pim kinase's structural information, aminopyrimidine was introduced to provide the hydrogen-bonding interactions with the conserved lysine residue in the ATP binding pocket of all three Pim kinases. Synthesized 3,5-bis(aminopyrimidinyl)indole derivatives showed pan-pim inhibitory activity. Aminoalkyl substituent was attached on the aminopyrimidine to further enhance the potency and physicochemical properties of compound. The research reveals a significative way of designing compounds with high potency and kinase selectivity for pan-pim kinases.

• Journal of Photoscience
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• v.9 no.2
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• pp.311-313
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• 2002

X-ray structures of pharaonis phoborhodopsin (ppR) show the different direction of the side chain of Arg72 from that of the corresponding residue (Arg82) of bacteriorhodopsin, BR. For BR, this residue is considered to play an important role in the proton pumping. In order to investigate the role of Arg72 in ppR, we constructed Arg72 mutants of R72A, R72K and R72Q, and measured the photocycle and proton pumping activities. The pH-titration curves on the absorption maximum of the mutants were shifted to alkaline in comparison of that of the wild-type. This may imply the increase of pKa of D75, suggesting the presence of the (probably electric) interaction between D75 and Arg72. Rate constants of the M-decay were 3-7 times faster than that of the wild-type, and the time for the completion of the photocycling was also reduced. Using Sn0$_2$ electrode, the rate of transmembrane proton transport was measured upon illumination. The photo-induced proton pumping activities were estimated after the corrections that are the percentages of the associated form of D75 (which has no pumping activity) and the photocycling rates. R72A and R72Q showed the reduced activity while R72K did not reduce the activity.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• Molecules and Cells
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• v.27 no.2
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• pp.149-157
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• 2009

In both gram-positive and several gram-negative bacteria, the transcription of dnaK and groE operons is negatively regulated by HrcA; however, the mechanism modulating HrcA protein activity upon thermal stress remains elusive. Here, we demonstrate that HrcA is modulated via reduction and oligomerization in vitro. Native-PAGE analysis was used to reveal the oligomeric structure of HrcA. The oligomeric HrcA structure became monomeric following treatment with the reducing agent dithothreitol, and this process was reversed by treatment with hydrogen peroxide. Moreover, the mutant HrcA C118S exhibited reduced binding to CIRCE elements and became less oligomerized, suggesting that cysteine residue 118 is important for CIRCE element binding as well as oligomerization. Conversely, HrcA mutant C280S exhibited increased oligomerization. An HrcA double mutant (C118S, C280S) was monomeric and exhibited a level of oligomerization and CIRCE binding similar to wild type HrcA, suggesting that cysteine residues 118 and 280 may function as checks to one another during oligomer formation. Biochemical fractionation of E. coli cells overexpressing HrcA revealed the presence of HrcA in the membrane fraction. Together, these results suggest that the two HrcA cysteine residues at positions 118 and 280 function as reduction sensors in the membrane and mediate oligomerization upon stress.