• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.379-392
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• 2007

• Bulletin of the Korean Chemical Society
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• v.32 no.spc8
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• pp.3149-3151
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• 2011

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.3-14
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• 2002

Functional genomics aims at uncovering useful information carried on genome sequences and at using it to understand the mechanisms of biological function. Elucidating the unknown biological functions of new genes based upon the genomics rationales will greatly speed up the extensive understanding of biocatalysis and biodegradation in biological world including microorganisms. DNA microarrays generate a system for the simultaneous measurement of the expression level of thousands of genes in a single hybridization assay. Their data mining (transcriptome) strategy has two categories: differential gene expression and coordinated gene expression. Furthermore, measurement of proteins (proteome) generates information on how the transcribed sequences end up as functional characteristics within the cell, and quantitation of metabolites yields information on how the functional proteins act to produce energy and process substrates (metabolome). Various composite functional genomics databases containing genetic, enzymatic and metabolic information have been developed and will contribute to the understanding of the life blue print and the new discoveries and practices in biocatalysis and biodegradation that could enrich their industrial and environmental applications.

• Journal of Microbiology and Biotechnology
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• v.33 no.3
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• pp.299-309
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• 2023

Glutathione peroxidases (Gpx) are a group of antioxidant enzymes that protect cells or tissues against damage from reactive oxygen species (ROS). The Gpx proteins identified in mammals exhibit high catalytic activity toward glutathione (GSH). In contrast, a variety of non-mammalian Gpx proteins from diverse organisms, including fungi, plants, insects, and rodent parasites, show specificity for thioredoxin (TRX) rather than GSH and are designated as TRX-dependent peroxiredoxins. However, the study of the properties of Gpx in the environmental microbiome or isolated bacteria is limited. In this study, we analyzed the Gpx sequences, identified the characteristics of sequences and structures, and found that the environmental microbiome Gpx proteins should be classified as TRX-dependent, Gpx-like peroxiredoxins. This classification is based on the following three items of evidence: i) the conservation of the peroxidatic Cys residue; ii) the existence and conservation of the resolving Cys residue that forms the disulfide bond with the peroxidatic cysteine; and iii) the absence of dimeric and tetrameric interface domains. The conservation/divergence pattern of all known bacterial Gpx-like proteins in public databases shows that they share common characteristics with that from the environmental microbiome and are also TRX-dependent. Moreover, phylogenetic analysis shows that the bacterial Gpx-like proteins exhibit a star-like radiating phylogenetic structure forming a highly diverse genetic pool of TRX-dependent, Gpx-like peroxidases.

• Biotechnology and Bioprocess Engineering:BBE
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• v.1 no.1
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• pp.46-50
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• 1996

In order to design industrial scale reactors and proceises for multi-phase biocatalytic reactions, it is essential to understand the mechanisms by which such systems operate. To il-lustrate how such mechanisms can be modeled, the hydrolysis of the primary ester groups of triglycerides to produce fatty acids and monoglycerides by lipased (glycerol-ester hydrolase) catalysis has been selected as an example of multiphase biocatalysis. Lipase is specific in its behavior such that it can act only on the hydrolyzed (or emulsified) part of the substrate. This follows because the active center of the enzyme is catalytically active only when the substrate contacts it in its hydrolyzed form. In other words, lipase acts only when it can shuttleback and forth between the emulsion phase and the water phase, presumably within an interphase or boundary layer between these two phases. In industrial applications lipase is employed as a fat splitting enzyme to remove fat stains from fabrics, in making cheese, to flavor milk products, and to degrade fats in waste products. Effective use of lipase in these processes requires a fundamental understanding of its kinetic behavior and interactions with substrates under various environmental conditions. Therefore, this study focuses on modeling and simulating the enzymatic activity of the lipase as a step towards the basic understanding of multi-phase biocatalysis processes.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2001.06a
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• pp.97-97
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• 2001

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.305-310
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• 2005

Internal motion of the protein has been described in many papers with C$_{\alpha}$ correlation coefficients to find motional correlation and functional characteristics. To describe the secondary structural motion and stability in protein, we have studied molecular dynamics (MD) simulations on FADD Death Domain and FADD Death Effector Domain which have a similar structure but have different functional characteristics. After 10ns MD simulations, the inter-helical motional correlations and the hydrogen bond ratios were compared between the two domains. From these data we could distinctly compare the internal motions of them and could explain the differences in experimental thermodynamic melting behaviors at molecular level.

• Journal of Microbiology and Biotechnology
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• v.25 no.6
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• pp.814-819
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• 2015

The natural crosslinking agent genipin has been applied widely in biomedicines and foods nowadays. Because of the special hemiacetal ring structure in its molecule, it can only be prepared by hydrolysis of geniposide according to biocatalysis. In this research, strategies including aqueous-organic biphasic catalysis and substrate fed-batch mode were adopted to improve the biocatalysis process of genipin. A 10 L ethyl acetate-aqueous biphasic system with geniposide fed-batch led to a satisfying genipin yield. With Fusarium solani ACCC 36223, 15.7 g/l genipin in the ethyl acetate phase was obtained, corresponding to space-time yields of 0.654 g l^-1 h^-1.

• Bulletin of the Korean Chemical Society
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• v.33 no.10
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• pp.3458-3460
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• 2012

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2003.06a
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• pp.124-124
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• 2003