• Biomedical Science Letters
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• v.9 no.4
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• pp.231-240
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• 2003

Deciphering the molecular interactions of proteins forming Z-lines is pivotal for understanding the regulation of myofibril assembly, sarcomeric organization, and mechanical properties of striated muscle. The purpose of this study is to searched for potential novel ligands of the Z-line portion of nebulin. In this study interacting proteins with intra-Z-line region of nebulin were screened using a yeast two-hybrid approach. The interaction was conformed by GST pull-down assay. We identified 269 residues within villin/gelsolin homology domain of supervillin that intreacts with the serine rich region of nebulin. The specific interactions of nebulin and supervillin were confirmed in vitro by GST pull-down experiments. Our data suggest that supervillin attaches directly to the Z-line through its interaction with the serine rich domain of nebulin in skeletal muscles. This interaction may link myofibrillar Z-discs to the membrane-associated complexes, costameres.

• BMB Reports
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• v.34 no.1
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• pp.85-89
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• 2001

Both topoisomerase $II{\alpha}$ and $II{\beta}$ east as phosphoproteins in the cells. Recently it was reported that DNA topoisomerase $II{\alpha}$ associates with and is phosphorylated by the extracellular signal-regulated kinase 2 (ERK2). Also, ERK2 stimulates the activity of topoisomerase II by a phosphorylation-independent manner [Shapiro et al., (1999) Mol. Cell. Biol. 19, 3551-3560]. In this study, a yeast two-hybrid system was used to investigate the binding site between topoisomerase $II{\alpha}$ or $II{\beta}$ and ERK2. The two-hybrid test clearly showed that topoisomerase $II{\beta}$ residues 1099-1263, and topoisomerase $II{\alpha}$ residues 1078-1182, mediate the interaction with ERK2, and that the leucine zipper motifs of topoisomerase $II{\alpha}$ and $II{\beta}$ are not required for its physical binding to ERK2. Our results suggest that topoisomerase $II{\beta}$ residues 1099-1263, and topoisomerase $II{\alpha}$ residues 1078-1182, may be common binding sites for activator proteins.

• Bulletin of the Korean Chemical Society
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• v.27 no.1
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• pp.87-92
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• 2006

Fas-associated death domain protein (FADD) recruits and activates procaspase-8 through interactions between the death effector domains of these two proteins. Cellular FLICE-inhibitory protein (c-FLIP) was identified as a molecule with sequence homology to caspase-8. It has been postulated that c-FLIP prevents formation of the competent death-inducing signaling complex in a ligand-dependent manner, through its interaction with FADD and/or caspase-8. However, the interaction of FADD and $c-FLIP_s$ (short form) in apoptosis signaling has been controversially discussed. We show the purification and the characterization of human full-length FADD and $c-FLIP_s$ expressed in Escherichia coli. The purified FADD and $c-FLIP_s$ are shown as homogeneity, respectively, in SDS-PAGE analysis and light-scattering measurements. The folding properties of the $\alpha$-helical structure of FADD and the super-secondary structure of $c-FLIP_s$ proteins were characterized by circular dichroism spectroscopy. Furthermore, we report here a series of biochemical and biophysical data for FADD-$c-FLIP_s$ binding in vitro. The binding of both FADD and $c-FLIP_s$ proteins was detected by BIAcore biosensor, fluorescence measurement, and size-exclusion column (SEC).

• Proceedings of the Earthquake Engineering Society of Korea Conference
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• 2003.09a
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• pp.481-488
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• 2003

A fluid-structure-isolator interaction program was developed in this study. The behavior of liquid regions are simulated by the boundary element method, and then the technique of analyzing the free surface motion in time domain is developed by using the nonlinear free surface boundary condition(NFBC) and the condition of interface between the structure and the fluid. Structure regions are modeled by the finite element method. In order to construct the governing equation of the fluid structure interaction(FSI)problem in time domain, the finite elements for a structure and boundary elements for liquid are coupled using the equilibrium condition, the compatibility condition and NFBC. The isolator is simulated by equation proposedin 3D Basis Me. In order to verify the validity and the applicability of the developed fluid- structure -Isolator interaction program, The horizontal forced vibration analysis was performed. The applicability of the developed method is verified through the artificial seismic analysis of real size liquid storage tank.

• Earthquakes and Structures
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• v.16 no.1
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• pp.109-118
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• 2019

This study, analyses the seismic response for a rigid massless square foundation resting on a viscoelastic soil layer limited by rigid bedrock. The foundation is subjected either to externally applied forces or to obliquely incident seismic body or surface harmonic seismic waves P, SV and SH. A 3-D frequency domain BEM formulation in conjunction with the thin layer method (TLM) is adapted here for the solution of elastodynamic problems and used for obtained the seismic response. The mathematical approach is based on the method of integral equations in the frequency domain using the formalism of Green's functions (Kausel and Peck 1982) for layered soil, the impedance functions are calculated by the compatibility condition. In this study, The key step is the characterization of the soil-foundation interaction with the input motion matrix. For each frequency the impedance matrix connects the applied forces to the resulting displacement, and the input motion matrix connects the displacement vector of the foundation to amplitudes of the free field motion. This approach has been applied to analyze the effect of soil-structure interaction on the seismic response of the foundation resting on a viscoelastic soil layer limited by rigid bedrock.

• BMB Reports
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• v.28 no.4
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• pp.363-367
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• 1995

E. coli methionyl-tRNA synthetase is one of the class I tRNA synthetases. The Tryptophane residue at the position 461 located in the C-terminal domain of the enzyme is a key amino acid for the interaction with the anticodon of $tRNA^{Met}$. W461 was replaced with other amino acids to determine the chemical requirement for the interaction with the anticodon of $tRNA^{Met}$. Saturation mutagenesis at the position 461 generated a total of 12 substitution mutants of methionyl-tRNA synthetase. All the mutants showed the same in vivo stability as the wild-type enzyme, suggesting that the amino acid substitutions did not cause severe conformational change of the protein The mutants containing tyrosine, phenylalanine, histidine and cysteine substitutions showed in vivo activity while all the other mutants did not. The comparison of the in vitro aminoacylation activities of these mutants showed that aromatic ring structure, Van der Waals volume and hydrogen bond potential of the amino acid residue at the position 461 are the major determinants for the interaction with the anticodon of $tRNA^{Met}$.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2001.04a
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• pp.309-314
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• 2001

In this study, the nonlinear soil structure interaction analysis method based on finite element and boundary element method is developed. In the seismic region, the nonlinearity of near field soil has to be considered for more exact reflection of soil-structure interaction effect. Thus, nonlinear finite element program coupled with boundary elements is developed for nonlinear soil-structure interaction analysis. Using the developed numerical algorithm, the nonlinear soil-structure interaction analysis is performed and responses due to dynamic forces and seismic excitation are investigated. The developed method is verified by comparing with previous studies.

• Proceedings of the Earthquake Engineering Society of Korea Conference
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• 2006.03a
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• pp.284-291
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• 2006

This paper presents a seismic response analysis of bridge structures considering foundation-soil interaction and multi-support input motion. In the earthquake analysis of structures it is usually assumed that the input ground motion is the same at all supports. However, this assumption is not justified for long structures like bridges, because observations have shown the earthquake ground motion can vary considerably within relatively small distances. When the soil under the foundation is relatively soft and deep, analysis for foundation-soil interaction always must be peformed. To consider foundation-soil interaction, soil response analysis is preceded, and after determining the material characteristics of foundation element obtained by foundation-soil interaction analysis at the frequency domain, the seismic response analysis of bridge superstructure with the equivalent spring and damper is performed. Finally, influences of multi-support input motion, which are affected by different soil characteristics, are also considered in this paper.

• Geomechanics and Engineering
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• v.23 no.6
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• pp.547-560
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• 2020

This paper studies the dynamic foundation-soil-foundation interaction for two square rigid foundations embedded in a viscoelastic soil layer. The vibrations come from only one rigid foundation placed in the soil layer and subjected to harmonic loads of translation, rocking, and torsion. The required dynamic response of rigid surface foundations constitutes the solution of the wave equations obtained by taking account of the conditions of interaction. The solution is formulated using the frequency domain Boundary Element Method (BEM) in conjunction with the Kausel-Peek Green's function for a layered stratum, with the aid of the Thin Layer Method (TLM), to study the dynamic interaction between adjacent foundations. This approach allows the establishment of a mathematical model that enables us to determine the dynamic displacements amplitude of adjacent foundations according to their different separations, the depth of the substratum, foundations masss, foundations embedded, and the frequencies of excitation. This paper attempts to introduce an approach based on a polynomial mathematical tool conducted from several results of numerical methods (BEM-TLM) so that practicing civil engineers can evaluation the dynamic foundations displacements more easy.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.3
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• pp.64-70
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• 2018

Human Tid1, belonging to the family of the Hsp40/DnaJ, functions as a co-chaperone of cytosolic and mitochondrial Hsp70 proteins. In addition, the conserved J-domain and G/F-rich region of Tid1 has been suggested to interact with the p53 tumor suppressor protein, to translocate it to the mitochondria. Here, backbone NMR assignments were achieved for the putative p53-binding domain of Tid1. The obtained chemical shift information identified five ${\alpha}$-helices including four helices characteristic of J-domain, which are connected to a short ${\alpha}$-helix in the G/F-rich region via a flexible loop region. We expect that this structural information would contribute to our progressing studies to elucidate atomic structure and molecular interaction of the domain with p53.