• Proceedings of the Zoological Society Korea Conference
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• 2001.10a
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• pp.239.1-239
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• 2001

No Abstract, See Full Text

• Proceedings of the Zoological Society Korea Conference
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• 2003.08a
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• pp.177.2-177
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• 2003

No Abstract, See Full Text

• Korea-Australia Rheology Journal
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• v.19 no.4
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• pp.233-242
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• 2007

We performed a numerical investigation to find out the optimal choice of the spatial discretization in the distributed-Lagrangian-multiplier/fictitious-domain (DLM/FD) method for the solid/fluid interaction problem. The elastic solid bar attached on the bottom in a pressure-driven channel flow of a Newtonian fluid was selected as a model problem. Our formulation is based on the scheme of Yu (2005) for the interaction between flexible bodies and fluid. A fixed regular rectangular discretization was applied for the description of solid and fluid domain by using the fictitious domain concept. The hydrodynamic interaction between solid and fluid was treated implicitly by the distributed Lagrangian multiplier method. Considering a simplified problem of the Stokes flow and the linearized elasticity, two numerical factors were investigated to clarify their effects and to find the optimum condition: the distribution of Lagrangian multipliers and the solid/fluid interfacial condition. The robustness of this method was verified through the mesh convergence and a pseudo-time step test. We found that the fluid stress in a fictitious solid domain can be neglected and that the Lagrangian multipliers are better to be applied on the entire solid domain. These results will be used to extend our study to systems of elastic particle in the Stokes flow, and of particles in the viscoelastic fluid.

• Molecules and Cells
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• v.27 no.3
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• pp.271-277
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• 2009

Proteins interact with each other within a cell, and those interactions give rise to the biological function and dynamical behavior of cellular systems. Generally, the protein interactions are temporal, spatial, or condition dependent in a specific cell, where only a small part of interactions usually take place under certain conditions. Recently, although a large amount of protein interaction data have been collected by high-throughput technologies, the interactions are recorded or summarized under various or different conditions and therefore cannot be directly used to identify signaling pathways or active networks, which are believed to work in specific cells under specific conditions. However, protein interactions activated under specific conditions may give hints to the biological process underlying corresponding phenotypes. In particular, responsive functional modules consist of protein interactions activated under specific conditions can provide insight into the mechanism underlying biological systems, e.g. protein interaction subnetworks found for certain diseases rather than normal conditions may help to discover potential biomarkers. From computational viewpoint, identifying responsive functional modules can be formulated as an optimization problem. Therefore, efficient computational methods for extracting responsive functional modules are strongly demanded due to the NP-hard nature of such a combinatorial problem. In this review, we first report recent advances in development of computational methods for extracting responsive functional modules or active pathways from protein interaction network and microarray data. Then from computational aspect, we discuss remaining obstacles and perspectives for this attractive and challenging topic in the area of systems biology.

• Journal of Microbiology
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• v.39 no.1
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• pp.24-30
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• 2001

In addition to effecting the catalysis of sugar uptake, the bacterial phosphoenolpyruvate::sugar phosphotransferase system regulates a variety of physiological processes. In a previous paper [Seok et al.,(1997) J. Biol. Chem. 272, 26511-26521], we reported the interaction with and allosteric regulation of Esiherichia coli glycogen phosphorylase activity by the histidine-containing phosphocarrier protein HPr in vitro. Here, we show that the specific interaction between HPr and glycogen phosphorylase occurs in vivo. To address the physiological role of the HPr-glycogen phosphorylase complex, intracellular glycogen levels were measured in E. coli strains transformed with various plasmids. While glycogen accumulated during the transition between exponential and stationary growth phases in wildtype cells, it did not accumulate in cells overproducing HPr or its inactive mutant regardless of the growth stage. From these results, we conclude that HPr mediates crosstalk between sugar uptake through the phosphoenolpyruvate:sugar phosphotransferase system and glycogen breakdown. The evolutionary significance of the HPr-glycogen phosphorylase complex is suggested.

• IMMUNE NETWORK
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• v.2 no.3
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• pp.125-132
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• 2002

In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.

• Korean Journal of Biological Psychiatry
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• v.17 no.2
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• pp.65-69
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• 2010

Gene-environment interactions are important in pathogenesis of suicide or suicidal behavior. Twin and adoption studies and family studies show that genetic factors play a critical role in suicide or suicidal behavior. Given the strong association between serotonergic neurotransmission and suicide, recent molecular genetic studies have focused on polymorphisms of serotonin genes, especially on serotonin transporter and tryptophan hydroxylase genes. Some studies have revealed a significant interaction between s allele of the serotonin transporter gene and the risk of suicide attempt associated with childhood trauma. In addition, the polymorphism of brain-derived neurotrophic factor gene also may influence the effect of childhood trauma in relation to the risk of attempting suicide. Future studies should explore genetic and environmental factors in suicide or suicidal behavior and examine for gene and environment interaction.

• Biomolecules & Therapeutics
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• v.32 no.4
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• pp.474-480
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• 2024

Streptomyces avermitilis genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid compounds. The recombinant CYP107P2 protein was expressed in Escherichia coli and the purified enzyme exhibited a typical P450 spectrum upon CO-binding in its reduced state. Type-I substrate-binding spectral titrations were observed with various terpenoid compounds, including α-pinene, β-pinene, α-terpinyl acetate, and (+)-3-carene. The calculated binding affinities (Kd) ranged from 15.9 to 50.8 µM. The X-ray crystal structure of CYP107P2 was determined at 1.99 Å resolution, with a well-conserved overall P450 folding conformation. The terpenoid compound docking models illustrated that the structural interaction between monoterpenes and CYP107P2, with the distance between heme and terpenes ranging from 3.4 to 5.4 Å, indicates potential substrate binding for P450 enzyme. This study suggests that CYP107P2 is a Streptomyces P450 enzyme capable of catalyzing terpenes as substrates, signifying noteworthy advancements in comprehending a novel P450 enzyme's involvement in terpene reactions.

• The Transactions of the Korean Institute of Electrical Engineers B
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• v.51 no.11
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• pp.616-621
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• 2002

With biological effects by ELF (Extremely Low Frequency) magnetic field generated from power system, the transient magnetic field from electric appliances is a major issue presently. Because the transient magnetic field induces higher current than the power frequency field inside living bodies, transient magnetic field exposure has been much focused. In this paper, it is shown that transient magnetic field from electric home appliances can be characterized as magnetic dipole moment. In this method, the dipole moment vector is assumed by allowing an uncertainty of 6dB in the estimated field. A parameter M that represents biological interaction was applied also. The proposed method was applied to 7 types of appliances (hair drier, heater, VDT, etc.) and their equivalent magnetic dipole moment and harmonic components were estimated. As the results, the useful data for quantifying magnetic field distribution around electric appliances were obtained.

• Proceedings of the Korean Biophysical Society Conference
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• 1999.06a
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• pp.43-43
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• 1999

Signal peptides of secretary proteins interact with various membranes and non-membrane components during the translocation. We investigated the interaction of signal peptides of ribose binding protein (RBP) with Escherichia coli (E.coli) signal recognition particle (SRP), SecA and lipid bilayer. Previous studies showed that the functional signal peptides inhibit the GTPase activity of E.coli SRP which consisted of F로 and 4.5S RNA.(omitted)