• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.5
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• pp.462-469
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• 2005

A top-down approach is known to be a useful and effective technique for the design and analysis of metabolic systems. In this Study, we have constructed a grouped metabolic network for Lactococcus lactis under aerobic conditions using grouped enzyme kinetics. To test the usefulness of grouping work, a non-grouped system and grouped systems were compared quantitatively with each other. Here, grouped Systems were designed as two groups according to the extent of grouping. The overall simulated flux values in grouped and non-grouped models had pretty similar distribution trends, but the details on flux ratio at the pyruvate branch point showed a little difference. This result indicates that our grouping technique can be used as a good model for complicated metabolic networks, however, for detailed analysis of metabolic network, a more robust mechanism Should be considered. In addition to the data for the pyruvate branch point analysis, Some major flux control coefficients were obtained in this research.

• Journal of Marine Bioscience and Biotechnology
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• v.2 no.1
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• pp.11-22
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• 2007

This aims to review natural products transformed by mimic intestinal metabolisms with microorganisms and hydrolytic enzymes, which exhibit enforced biological activity, higher extraction yield and identification of active components. In the process, transformation to the smaller active compounds with enzymes and microbes mimics the pharmacological action of natural products by intestinal bacteria. In order to establish conditions for the fermentation and enzyme reaction, it is required to choose several natural products for biotransformation and investigate the optimal conditions for the fermentation or the enzyme reaction such as composition, temperature, pH, inoculum, and cultivation time. It is expected an increase of the internal absorption of the active materials without regard to the intestinal microbes or its ability through biosynthesis of the active materials by the microbes and enzymes. And this techniques can be applied to biotransformation of natural products such as sesaminol, resveratrol, 1-deoxy nojirimycin, naringenin, quercetin, and baicalin and to the metabolism study using the animal model.

• International Journal of Vascular Biomedical Engineering
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• v.4 no.2
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• pp.13-18
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• 2006

Direct injection of a fibrinolytic agent to the intra-arterial thrombosis may increase the effectiveness of thrombolysis by enhancing the permeation of thrombolytic agents into the blood clot. Permeation of fibrinolytic agents into a clot is influenced by the surface pressure, which is determined by the injection velocity of fibrinolytic agents. Computational fluid dynamic methods were used in order to predict clot lysis for different jet velocities and nozzle arrangements. Firstly, thrombolysis of a clot was mathematically modeled based on the pressure and lysis front velocity relationship. Direct injection of a thrombolytic agent increased the speed of thrombolysis significantly and the effectiveness was increased as the ejecting velocity increased. The nine nozzles model showed about 20% increase of the lysed volume, and the one and seventeen nozzles models did not show significant differences. Secondly, thrombolysis was modeled based on the enzyme transport and the fluid flow equations, and quasi steady numerical analysis was performed. Clot lysis efficiency was also increased as injection velocity increased.

• Korean Journal of Food Science and Technology
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• v.23 no.2
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• pp.224-228
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• 1991

The effect of linoleate hydroperoxides(LAHPO) on pepsin activity was investigated. The activity of pepsin was largely decreased by LAHPO at various temperatures and pH. The inactivation of pepsin seems to be the radicals in the system because ascorbate and metal ions enhanced the inactivation of enzyme by LAHPO. It was shown by SDS-PAGE that LAHPO caused scission of the enzyme in the model system.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.212-216
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• 2015

Oseltamivir, also known as Tamifu, is an inhibitor of neuraminidase protein which plays an essential role in proliferation and replication of influenza virus. Binding to the active site of neuraminidase, the oseltamivir prevents the protein from enzyme reaction. Conformational change of the protein(neuraminidase) should be accompanied by the enzyme reaction, but the drug inhibits the protein to deform. In this study, we examine the influence of oseltamivir on protein's conformational change in the structural and mechanical point of view. Finite element analysis of the protein can be an useful approach to investigate the influence of oseltamivir on the deformation of a protein. We suggest the finite element based protein model, and then perform the linear static analysis with the displacement loading condition based on the first two largest motion which can be obtained from the normal mode analysis. The results show that it takes more energy to change shape of the protein with an oseltamivir attached than the protein without an oseltamivir.

• Mycobiology
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• v.39 no.4
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• pp.243-248
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• 2011

The ubiquitin-proteasome system is one of the major protein turnover mechanisms that plays important roles in the regulation of a variety of cellular functions. It is composed of E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 ubiquitin ligases that transfer ubiquitin to the substrates that are subjected to degradation in the 26S proteasome. The Skp1, Cullin, F-box protein (SCF) E3 ligases are the largest E3 gene family, in which the F-box protein is the key component to determine substrate specificity. Although the SCF E3 ligase and its F-box proteins have been extensively studied in the model yeast Saccharomyces cerevisiae, only limited studies have been reported on the role of F-box proteins in other fungi. Recently, a number of studies revealed that F-box proteins are required for fungal pathogenicity. In this communication, we review the current understanding of F-box proteins in pathogenic fungi.

• Bulletin of the Korean Chemical Society
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• v.4 no.2
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• pp.72-76
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• 1983

Cephaloglycin was synthesized directly from D-${\alpha}$ -phenylglycine methyl ester and 7-aminocephalosporanic acid using whole cell enzyme of Xanthomonas citri (IFO 3835). Some optimal conditions for cephaloglycin synthesis were investigated, and yield improvements for its production by several methods were attempted. Using the whole cell enzyme system, the reaction kinetic model for cephaloglycin synthesis is proposed, and the kinetic constants for D-${\alpha}$ -phenylglycine methyl ester hydrolysis, cephaloglycin synthesis, and cephaloglycin hydrolysis were determined. The $K_m$ values of D-${\alpha}$-phenylglycine methyl ester, 7-aminocephalosporanic acid, and cephaloglycin were 11 mM, 24 mM, and 167 mM, and $K_i$ value of D-${\alpha}$-phenylglycine was 15 mM, respectively. The pattern of product inhibition was found to be competitive one.

• Journal of the Korea Society of Computer and Information
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• v.27 no.8
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• pp.49-59
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• 2022

In this paper, we designed a new enzyme function prediction model PSCREM based on a study that compared and evaluated CNN and LSTM/GRU models, which are the most widely used deep learning models in the field of predicting functions and structures using protein sequences in 2020, under the same conditions. Sequence evolution information was used to preserve detailed patterns which would miss in CNN convolution, and the relationship information between amino acids with functional significance was extracted through overlapping RNNs. It was referenced to feature map production. The RNN family of algorithms used in small CNN-RNN models are LSTM algorithms and GRU algorithms, which are usually stacked two to three times over 100 units, but in this paper, small RNNs consisting of 10 and 20 units are overlapped. The model used the PSSM profile, which is transformed from protein sequence data. The experiment proved 86.4% the performance for the problem of predicting the main classes of enzyme number, and it was confirmed that the performance was 84.4% accurate up to the sub-sub classes of enzyme number. Thus, PSCREM better identifies unique patterns related to protein function through overlapped RNN, and Overlapped RNN is proposed as a novel methodology for protein function and structure prediction extraction.

• Microbiology and Biotechnology Letters
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• v.46 no.3
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• pp.234-243
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• 2018

The Antarctic Ocean contains numerous microorganisms that produce novel biocatalysts that can have applications in various industries. We screened various psychrophilic bacterial strains isolated from the Ross Sea and found that a Croceibacter atlanticus strain (Stock No. 40-F12) showed high lipolytic activity on a tributyrin plate. We isolated the corresponding lipase gene (lipCA) by shotgun cloning and expressed the LipCA enzyme in Escherichia coli cells. Homology modeling of LipCA was carried out using the Spain Arreo lake metagenome alpha/beta hydrolase as a template. According to the model, LipCA has an ${\alpha}/{\beta}$ hydrolase fold, Gly-X-Ser-X-Glymotif, and lid sequence, indicating that LipCA is a typical lipase enzyme. Active LipCA enzyme was purified fromthe cell-free extract by ammonium sulfate precipitation and gel filtration chromatography. We determined its enzymatic properties including optimum temperature and pH, stability, substrate specificity, and organic solvent stability. LipCA was immobilized by the cross-linked enzyme aggregate (CLEA) method and its enzymatic properties were compared to those of free LipCA. After cross-linking, temperature, pH, and organic solvent stability increased considerably, whereas substrate specificities did not changed. The LipCA CLEA was recovered by centrifugation and showed approximately 40% activity after 4th recovery. This is the first report of the expression, characterization, and immobilization of a C. atlanticus lipase, and this lipase could have potential industrial application.

• The Korean Journal of Physiology and Pharmacology
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• v.18 no.3
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• pp.269-278
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• 2014

Various antiepileptic drugs (AEDs) especially enzyme-inducing AEDs might be associated with increased vascular risk, through impairment of the endogenous antioxidative ability which may trigger oxygen-dependent tissue injury. Lamotrigine (LTG) a non-enzyme-inducing AED has scarce information regarding its effects on oxidative stress. The present study aimed to study the possible modulation of vascular risk factors of epileptogenesis by LTG, in a rat model of kindling seizure induced by pentylenetetrazole (PTZ). Four groups of male Wister rats were used; vehicle control group, PTZ group (alternate day PTZ, 30 mg/kg, i.p), LTG/PTZ group (LTG 20 mg/kg/day p.o and alternate day PTZ) and LTG group. The study period was 5 weeks. Lipoproteins and total homocysteine (tHcy), malondialdehyde (MDA) and reduced glutathione (GSH) were measured. Aortic endothelial function study and histopathological examination of the rats' brains, aortas and coronaries were conducted. Serum total cholesterol (TC), triglyceride (TG) and low-density lipoprotein cholesterol (LDL-C), tHcy, MDA, GSH levels were significantly higher in epileptic rats than normal controls rats. A decrease in HDL-cholesterol with high atherosclerotic index was also demonstrated. The administration of LTG improved the PTZ-kindled seizures. It produced a significant decrease in TC, TG and LDL-cholesterol, MDA, aortic GSH and increase in HDL-cholesterol with no significant effect on serum GSH and tHcy levels. LTG improved endothelium-dependent relaxation, decreased hippocampal neurodegenerative changes and atherosclerotic changes of aortas and coronaries. LTG decreased seizures severity, hippocampal damage and improved vascular risk markers in this rat model of kindling seizures.