• Bulletin of the Korean Chemical Society
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• v.33 no.10
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• pp.3248-3252
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• 2012

Vibrio extracellular metalloprotease (vEP), secreted from Vibrio vulnificus, shows various proteolytic function such as prothrombin activation and fibrinolytic activities. Premature form of vEP has an N-terminal (nPP) and a C-terminal (C-ter100) region. The nPP and C-ter100 regions are autocleaved for the matured metalloprotease activity. It has been proposed that two regions play a key role in regulating enzymatic activity of vEP. Especially, C-ter100 has a regulatory function on proteolytic activity of vEP. C-ter100 domain has been cloned into the E. coli expression vectors, pET32a and pGEX 4T-1 with TEV protease cleavage site and purified using gel-filtration chromatography followed by affinity chromatography. To understand how C-ter100 modulates proteolytic activity of vEP, structural studies were performed by heteronuclar multi-dimensional NMR spectroscopy. Backbone $^1H$, $^{15}N$ and $^{13}C$ resonances were assigned by data from standard triple resonance and HCCH-TOCSY experiments. The secondary structures of vEP C-ter100 were determined by TALOS+ and CSI software based on hydrogen/deuterium exchange. NMR data show that C-ter100 of vEP forms a ${\beta}$-barrel structure consisting of eight ${\beta}$-strands.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.1
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• pp.22-33
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• 2012

Tid1, belonging to the Hsp40/DnaJ family of proteins, functions as a cochaperone of cytosolic and mitochondrial Hsp70 proteins. In particular, the N-terminal J-domain of Tid1 (Tid1-JD) constitutes the major binding sites for proteinprotein interactions with client proteins, including p53, as well as its partner chaperone, Hsp70. In the present study, soluble, recombinant protein of Tid1-JD could be obtained by using the pCold vector system, and backbone NMR assignments were completed using the isotope $[^{13}C/^{15}N]$-enriched protein. Far-UV CD result implied that Tid1-JD is an ${\alpha}$-helical protein and the secondary structure determined using chemical shift data sets indentified four ${\alpha}$-helices with a loop region containing the HPD (conserved tripeptide of His, Pro and Asp) motif. Additionally, NMR spectra under different conditions implied that the HPD motif, which is a critical region for protein-protein interactions of Tid1-JD, would possess dynamic properties.

• BMB Reports
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• v.42 no.6
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• pp.387-392
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• 2009

Here, we report the first biochemical and structural characterization of the hypothetical protein HP0902 from Helicobacter pylori, in terms of structural genomics. Gel-permeation chromatography and dynamic light scattering indicated that the protein behaves as a dimer in solution. Circular dichroism spectroscopy showed that HP0902 primarily adopts a $\beta$-structure and the protein was highly thermostable with a denaturing temperature higher than $70^{\circ}C$. Finally, the backbone NMR assignments were obtained on the [$^{13}C,^{15}N$]HP0902 and the secondary structure was determined using the chemical shift data. Additionally, the local flexibility was assessed via a heteronuclear $^1H-^{15}N$ steady state NOE experiment. The results revealed that HP0902 would adopt a compactly folded, all-$\beta$ topology with 11 $\beta$-strands. All of the results clearly support the notion that HP0902 belongs to the cupin superfamily of proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.2
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• pp.162-171
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• 2012

SAV2228 has an OB (Oligomer-Binding)-motif which is frequently used for nucleic acid recognition. To characterize the activity of translation initiation factor-1 (IF-1) from Staphylococcus aureus, SAV2228 was expressed and purified in Escherichia coli. We acquired 3D NMR spectra showing well dispersed and homogeneous signals which allow us to assign 94.4% of all $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$ and $^{13}CO$ resonances. We could predict a secondary structure of SAV2228 using TALOS and CSI from NMR data. SAV2228 was consisted of one ${\alpha}$-helix and five ${\beta}$-sheets. The predicted secondary structure, ${\beta}-{\beta}-{\beta}-{\alpha}-{\beta}-{\beta}$, was similar to other bacterial IF-1, but it was not completely same to the eukaryotic one. Assigned NMR peaks and secondary structre prediction can be used for the study on interaction with nucleic acid in the future.

• 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.16 no.3
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• pp.341-345
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• 2010

WMN is one of efficient solutions to provide Internet services for users by forming wireless backbone networks with wireless links. The dominant technology for WMNs is the IEEE 802.11, which provides multi-channel and multi-rate capabilities. One of important issues in WMNs is the network capacity and it is essential to design a multi-channel protocol that leverages the network capacity. However, when wireless links that use different data rates operate on the common channel, the performance of high-rate links is severely degraded by the presence of the low-rate links, which is often referred as performance anomaly. In this paper, we propose a Tree-based Channel Assignment (TreeCA) protocol to mitigate the performance anomaly problem by distributing data rates over multiple channels. TreeCA performs channel assignments based on the tree WMN architecture to accommodate the Internet traffics efficiently. Parent nodes on the tree distribute their child nodes over multiple channels so that the performance anomaly is reduced. Through simulations, we observed that the proposed TreeCA outperforms the existing multi-channel protocols for WMNs.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.35 no.12A
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• pp.1152-1159
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• 2010

Wireless Mesh Networks (WMNs) provides Internet accesses to users by forming backbone networks via wireless links. A key problem of WMN is network capacity. For this, multi-channel and multi-rate functions of IEEE 802.11 can be utilized. Depending on channel assignments, multi-channel determines node connectivity and channel diversity. Also, in IEEE 802.11 multi-rate networks, the rate anomaly problem occurs, the phenomenon that low-rate links degrades the performance of high-rate links. In this paper, we propose rate separating multi-channel (RSMC) protocols that improves the node connectivity and channel diversity, and mitigates the rate anomaly problem. RSMC increases the channel diversity by forming tree-based WMNs and decreases the rate anomaly by separating different rate links on the tree via channels. In addition, it uses network connectivity (NC) algorithm to increase the node connectivity. Through simulations, we demonstrate that the RSMC shows improved performance than existing multi-channel protocols in terms of aggregate throughput, node connectivity, channel diversity.

• Journal of KIISE:Information Networking
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• v.37 no.5
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• pp.374-385
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• 2010

Wireless mesh networks can be deployed for various networks from home networking to last-mile broadband Internet access. Wireless mesh networks are composed of mesh routers and mesh clients. In these networks, static nodes form a multi-hop backbone of a large wireless access network that provides connectivity to end-users' mobile terminals. The network nodes cooperate with each other to relay data traffic to its destinations. In order to increase connectivity and better performance, researchers are getting interested in multi-channel and multi-interface wireless mesh networks. In these networks, non-overlapping multiple frequency channels are used simultaneously to increase the aggregate bandwidth available to end-users. Recently, researches have focused on finding suitable channel assignments for wireless network interfaces, equiped in a mesh node, together with efficient routing to improve overall system throughput in wireless mesh networks. This goal can be achieved by minimize channel interference. Less interference among using channels in a network guarantees more aggregated channel capacity and better connectivity of the networks. In this thesis, we propose interference aware channel assignment and routing algorithms for multi-channel multi-hop wireless mesh networks. We propose Channel Assignment and Routing algorithms using Traffic Profiles(CARTP) and Routing algorithms allowing detour routing(CARTP+2). Finally, we evaluate the performance of proposed algorithms in comparison to results from previous methods using ns-2 simulations. The simulation results show that our proposed algorithms can enhance the overall network performance in wireless mesh networks.