• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.70-70
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• 2003

Active sites and substrate bindings of 1-aminoxyclopropane-1-carboxylate oxidase (MD-ACO1) catalyzing the oxidative conversion of ACC to ethylene have been determined based on site-directed mutagenesis and comparative modeling methods. Molecular modeling based on the crystal structure of Isopenicillin N synthase (IPNS) provided MD-ACO1 structure. MD-ACO1 protein folds into a compact jelly roll shape, consisting of 9 ${\alpha}$-helices, 10 ${\beta}$-strands and several long loops. The MD-ACO1/ACC/Fe(II)/Ascorbate complex conformation was determined from automated docking program, AUTODOCK. The MD-ACO1/Fell complex model was consistent with well known binding motif information (HIS177-ASP179-HIS234). The cosubstrate, ascorbate is placed between iron binding pocket and Arg244 of MD-ACO1 enzyme, supporting the critical role of Arg244 for generating reaction product. These findings are strongly supported by previous biochemical data as well as site-directed mutagenesis data. The structure of enzyme/substrate suggests the structural mechanism for the biochemical role as well as substrate specificity of MD-ACO1 enzyme.

• Current Applied Physics
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• v.18 no.12
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• pp.1507-1512
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• 2018

The development of an organic-based aqueous redox flow battery (RFB) using quinone as an electroactive material has attracted great attention recently. This is because this battery is inexpensive, produces high energy density, and is environment friendly in stationary electrical energy storage applications. Herein, we investigate the redox potentials and solubilities of indole-5,6-quinone and indole-4,7-quinone derivatives in terms of the substituent effects of functional groups using theoretical calculations. Our results indicate that full-site substituted derivatives of indolequinone are more useful as active materials compared to single-site substituted derivatives. In particular, our calculations reveal that the substitution of $-PO_3H_2$ and $-SO_3H$ functional groups with multiple polar bonds is very effective in increasing the activity of the aqueous RFB. As a strategy to overcome the limitation that the aqueous solubility is intrinsically low because they are organic molecules, we suggest the substitution of functional groups with multiple polar bonds to the backbones of active organic materials. Among 180 indolequinone derivatives, 17 candidates that meet the redox potential standards ($${\leq_-}0.2V$$ or $${\geq_-}0.9V$$) and eight candidates with solubility exceeding 2 mol/L are identified. Three indolequinone derivatives that satisfy both conditions are finally presented as promising electroactive candidates for an aqueous RFB.

• Journal of Environmental Science International
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• v.14 no.5
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• pp.457-461
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• 2005

The survey of user's satisfactory degree of location, plantings, facilities, operation, and management factors on national parks' camp sites was carried out. Many problems were analyzed and identified. This survey was for proposing the correct way to plan and draft for camping site after this. In addition to, the realization of environmental education through nature friendly recreation was aimed at. According to the result of the survey, the followings were suggested as necessities to improve the camp site. 1. Repair and replacement of insufficiently managed facilities should be aimed at. 2. Facilities for a handicapped person should be preferentially introduced. 3. Active management and publicity in low-demand season that practiced by developed countries should be carried out. Seasonal program for various age groups should be operated. 4. Surrounding tourist site, camp site, and trail should be organically connected by shuttle bus and other transports. A survey was carried out for the user satisfaction in the campsites of national parks. Based on this survey concerned with the location, planting, facilities, operation and management, the problems were identified and analysed to improve future design and plan of the campsites. This study aims for the realization of environmental education through nature friendly recreation. The following points are suggested as needed according to the survey result. 1. damaged facilities should be repaired or replaced. 2. introduction of the facilities for disabled should be prioritized. 3. consistent and active management and publicity work should be operated in the off-peak season. and the seasonal activity programs for the various age groups should be provided. 4. the site should be well connected with other surrounding campsites and tourist sites using the shuttle bus and other transport method.

• Proceedings of the KIEE Conference
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• 2007.11b
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• pp.162-164
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• 2007

This paper presents a HVDC site selection algorithm to increase transfer capability using VSC HVDC system which can control active power as well as reactive power. Using normal powerflow results and simple index $k_r$ the HVDC site selection algorithm is enhanced and more tightly-coupled transmission lines are identified in a domain of generators.

• Korean Journal of Microbiology
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• v.29 no.4
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• pp.209-214
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• 1991

The PRD1 DNA polymerase is a small multi-functional enzyme containing conserved amino acid sequences shared by family B DNA polymerases. Thus the PRD1 DNA polymerase provides an useful model system with which to study structure-functional relationships of DNA polymerase molecules. In order to investigate the functional and structural roles of the highly conserved amino acid sequences, we have introduced three mutations into a conserved amino acid of the PRD1 DNA polymerase. Genetic complememtation study indicated that each mutation inactivated DNA polymerase catalytic activity.

• Microbiology and Biotechnology Letters
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• v.34 no.2
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• pp.121-128
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• 2006

The purified xylanase from Bacillus alcalophilus AX2000 was modified with various chemical modifiers to determine amino acid residues in the active site of the enzyme. Treatment of the enzyme with group-specific reagents such as carbodiimide or N-bromosuccinimide resulted in complete loss of enzyme activity. These results suggested that these reagents reacted with glutamic acid or aspartic acid and tryptophan residues located at or near the active site. In each case, inactivation was performed by pseudo first-order kinetics. Inhibition of enzyme activity by carbodiimide and N-bromosuccinimide showed non-competitive and competitive inhibition type, respectively. Addition of xylan to the enzyme solution containing N-bromosuccinimide prevented the inactivation, indicating the presence of tryptophan at the substrate binding site. Analysis of kinetics for inactivation showed that the loss of enzyme activity was due to modification of two glutamic acid or aspartic acid residues and single tryptophan residue.

• The KIPS Transactions:PartD
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• v.14D no.7
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• pp.743-752
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• 2007

Proteins combine with other materials to achieve their function and have similar function if their active sites are similar. Thus we can infer the function of protein by identifying the binding area of proteins. This paper suggests the novel method to select binding area of protein using MCL (Markov Cluster) algorithm. We construct the distance matrix from surface residues distance on protein. Then this distance matrix is transformed to connectivity matrix for applying MCL process. We adopted Catalytic Site Atlas (CSA) data to evaluate the proposed method. In the experimental result using CSA data (94 selected single chain proteins), our algorithm detects the 91 (97%) binding area near by active site of each protein. We introduced a new geometrical features and this mainly contributes to reduce the time to analyze the protein by selecting the residues near by active site.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.619-619
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• 2005

• Proceedings of the Zoological Society Korea Conference
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• 1994.10a
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• pp.203.1-203
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• 1994

No Abstract, See Full Text

• BMB Reports
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• v.40 no.3
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• pp.315-324
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• 2007

The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.