• Journal of the Korean Magnetic Resonance Society
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• v.21 no.3
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• pp.109-113
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• 2017

The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5'-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized $^{13}C$- and $^{15}N$-double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.

• Bulletin of the Korean Chemical Society
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• v.30 no.5
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• pp.1043-1046
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• 2009

Human protein tyrosine kinase-6 (PTK6) is a member of the non-receptor protein tyrosine kinase family and it is found in two-thirds of all breast tumors. Very recently, we proposed that the SH3 domain of PTK6 interacts with the linker region (Linker) between the SH2 and kinase domains, proving that the interaction between SH3 domain and Linker plays an important role in auto-inhibition mechanism. Residues from 1 to 191 corresponding region of SH3-SH2-Linker (SH32L) of PTK6 was cloned into the pET32a expression vector with Tobbaco etch virus (TEV) protease enzyme site by sequence homology and 3D structural model. The purified PTK6-SH32L was determined as a monomer conformation in solution. The amide proton resonances in the $^{15}N-^{1}H$ 2D-HSQC spectrum suggest that PTK6-SH32L possesses disordered structural region of the flexible/unstructured linker region. In addition, the backbone amide proton chemical shifts of the SH3 domain in the PTK6-SH32L differ from that of the independent domain, indicating that intra-molecular interaction between SH3 and Linker in the PTK6-SH32L is present.

• Journal of the Korean Magnetic Resonance Society
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• v.26 no.3
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• pp.34-39
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• 2022

The SH3 domain found within a variety of proteins is comprised of generally 60 residues, and participated in protein-protein interactions with proline-rich motifs. Cobll1 was identified as a distinct molecular marker associated with CML progression, and PACSIN2 was discovered a novel Cobll1 binding partner through direct interaction between a SH3 domain of PACSIN2 and three proline-rich motifs of Cobll1. To understand the structural basis of interactions between PACSIN2 and Cobll1, backbone assignments of PACSIN2 SH3 domain were performed. Furthermore, three proline-rich peptides of Cobll1 were titrated to ¹⁵N-labeled PACSIN2 SH3 domain in various ratios. Our chemical shift changes data and conserved SH3 sequence alignment will be helpful to analyze fundamental molecular basis related to the interaction between PACSIN2 and Cobll1.

• Journal of KIISE:Computing Practices and Letters
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• v.11 no.5
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• pp.427-435
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• 2005

With the accumulation of protein and its related data on the Internet, many domain based computational techniques to predict protein interactions have been developed. However, most of the techniques still have many limitations to be used in real fields. They usually suffer from a low accuracy problem in prediction and do not provide any interaction possibility ranking method for multiple protein pairs. In this paper, we reevaluate a domain combination based protein interaction prediction method and develop an interaction possibility ranking method for multiple protein pairs. Probability equations are devised and proposed in the framework of domain combination based protein interaction prediction method. Using the ranking method, one can discern which protein pair is more probable to interact with each other than other protein pairs in multiple protein pairs. In the validation of the ranking method, we revealed that there exist some correlations between the interacting probability and the precision of the prediction in case of the protein pair group having the matching PIP(Primary Interaction Probability) values in the interacting or non interacting PIP distributions.

• Proceedings of the Korean Biophysical Society Conference
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• 1998.06a
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• pp.12-12
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• 1998

The interaction between the N-terminal domain of enzyme I (EIN) and the histidine-containing phosphocarrier protein HPr of the Escherichia coli phosphoenolpyruvate：sugar phosphotransferase system has been investigated by Isothermal Titration Calorimetry and heteronuclear magnetic resonance spectroscopy.(omitted)

• Proceedings of the Earthquake Engineering Society of Korea Conference
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• 1999.10a
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• pp.107-112
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• 1999

This paper presents a time domain method for soil-structure interaction analysis for seismic loadings. It is based on the finite element formulation incorporating analytical frequency-dependent infinite elements for the far-field soil. The dynamic stiffness matrices of the far-field region formulated in frequency domain using the present method can be easily transformed into the corresponding matrices in time domain. Hence the response can be analytical computed in time domain. Example analysis has been carried out to verify the present method for an embedded block in a multi-layered half-space. The present methods can be easily extended to the nonlinear analysis since the response analysis is carried out in time domain.

• Proceedings of the Korean Magnestics Society Conference
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• 2015.05a
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• pp.78-79
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• 2015

We investigate the switching current for various cell diameters and DM interaction. We find that the current density for switching can depend strongly on the cell size when the switching is governed by the domain wall motion. Moreover the switching current density is also strongly influenced by DM interaction. In the presentation, we will discuss the effect of domain wall formation and more various DMI constant on the switching current desity in detail.

• 한국HCI학회:학술대회논문집
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• 2009.02a
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• pp.677-684
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• 2009

With various sensor network and ubiquitous technologies, we can extend interaction area from a virtual domain to physical space domain. This spatial interaction is differ in that traditional interaction is mainly processed by direct interaction with the computer machine which is a target machine or provides interaction tools and the spatial interaction is performed indirectly between users with smart interaction tools and many distributed components of space. So, this interaction gives methods to users to control whole manageable space components by registering and recognizing objects. Finally, this paper provides an effective spatial interaction method with template-based task mapping algorithm which is sorted by historical interaction data for support of users' intended task. And then, we analyze how much the system performance would be improved with the task mapping algorithm and conclude with an introduction of a GUI method to visualize results of spatial interaction.

• Biomedical Science Letters
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• v.9 no.2
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• pp.105-110
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• 2003

Ankyrins are a ubiquitously expressed family of intracellular adaptor proteins involved in targeting diverse proteins to specialized membrane domains in both the plasma membrane and the endoplasmic reticulum. Canonical ankyrins are 190-220 kDa proteins expressed in most tissues and cell types and comprise a membrane-binding domain (MBD) of 24 ANK repeats, a spectrin-binding domain, a death domain and a C-terminal domain. Rescue studies with ankyrin-B/G chimeras have identified the C-terminal domain of ankyrin-B as the defining domain in specifying ankyrin-B activity, but the function of C-terminal domain of ankyrin-B is, however, not known. We report here that the C-terminal domain of ankyrin-B is capable of interacting with the C-terminal Region of Hsp40. The Hsps are induced not only by heat shock but also by various other environmental stresses. Hsps are also expressed constitutively at normal growth temperatures and have basic and indispensable functions in the life cycle of proteins as molecular chaperones, as well as playing a role in protecting cells from the deleterious stresses. The binding sites required in the interaction between C-terminal domain of ankyrin-B and C-terminal region of Hsp40 were characterized using the yeast two-hybrid system and GST-pull down assay. The interaction between ankyrin-B and Hsp40 represents the first direct evidence of ankyrin's role as chaperones.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2008.04a
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• pp.14-19
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• 2008

This paper presents dynamic infinite element formulations which have been developed for soil-structure interaction analysis both in frequency and in time domains by the present authors during the past twenty years. Axisymmetric, 2D and 3D layered half-space soil media were considered in the developments. The displacement shape functions of the infinite elements were established using approximate expressions of analytical solutions in frequency domain to represent the characteristics of multiple waves propagating into the unbounded outer domain of the media. The proposed infinite elements were verified using benchmark examples, which showed that the present formulations are very effective for the soil-structure interaction analysis either in frequency or in time domain. Example applications to actual interaction problems are also given to demonstrate the capability and versatility of the present methodology.