• BMB Reports
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• v.40 no.5
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• pp.839-843
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• 2007

HP0495 (Swiss-Prot ID; Y495_HELPY) is an 86-residue hypothetical protein from Helicobacter pylori strain 26695. The function of HP0495 cannot be identified based on sequence homology, and HP0495 is included in a fairly unique sequence family. Here, we report the sequencespecific backbone resonance assignments of HP0495. About 97% of all the $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances were assigned unambiguously. We could predict the secondary structure of HP0495, by analyzing the deviation of the $^{13}C{\alpha}$ and $^{13}C{\beta}$ shemical shifts from their respective random coil values. Secondary structure prediction shows that HP0495 consists of two $\alpha$-helices and four $\beta$-strands. This study is a prerequisite for determining the solution structure of HP0495 and investigating the protein-protein interaction between HP0495 and other Helicobacter pylori proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.12 no.2
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• pp.65-73
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• 2008

HP1298 (Swiss-Prot ID ; P65108) is an 72-residue protein from Helicobacter pylori strain 26695. The function of HP1298 was identified as Translation initiation factor IF-l based on sequence homology, and HP1298 is included in IF-l family. Here, we report the sequence-specific backbone resonance assignments of HP1298. About 97% of all the $^{1}HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances could be assigned unambiguously. We could predict the secondary structure of HP1298, by analyzing the deviation of the $^{13}C{\alpha}$ and $^{13}C{\beta}$ shemical shifts from their respective random coil values. Secondary structure prediction shows that HP1298 consists of six $\beta$-strands. This study is a prerequisite for determining the solution structure of HP1298 and investigating the structure-function relationship of HP1298. Assigned chemical shift can be used for the study on interaction between HP1298 and other Helicobacter pylori proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.27 no.4
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• pp.23-27
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• 2023

Hoxc, or the Homeobox C cluster, is a group of genes that play a crucial role in embryonic development, particularly in patterning the body along the anterior-posterior axis. These genes encode transcription factors, which are proteins that bind to DNA and regulate the expression of other genes. Hoxc9 is specifically involved in the development of the skeletal system, nervous system, and adipose tissue. Hoxc9 overexpression has been linked to the development of various cancers such as leukemia and breast cancer. Here, we assigned the chemical shifts Hoxc9 DNA binding domain (DBD) using heteronuclear NMR techniques. The helical regions of Hoxc9 DBD correspond to the residues T200 - F213 (Helix I), T218 - L229 (Helix II), and T232 - K249 (Helix III). Our result would be helpful for studing the molecular interactions of the Hoxc9 DBD and other proteins.

• Molecules and Cells
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• v.27 no.4
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• pp.493-496
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• 2009

Hypoxia-inducible factor $1{\alpha}$ ($HIF1{\alpha}$) is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of $HIF1{\alpha}$ responsible for the negative regulation of $HIF1{\alpha}$ in normoxia is intrinsically unfolded. Here, we carried out the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignment of a proteolysis-resistant fragment (residues 404-477) in the $HIF1{\alpha}$ ODD domain using NMR spectroscopy. About 98% (344/352) of all the $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances were unambiguously assigned. The results will be useful for further investigation of the structural and dynamic states of the $HIF1{\alpha}$ ODD domain and its interaction with binding partners.

• Journal of the Korean Magnetic Resonance Society
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• v.28 no.2
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• pp.6-9
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• 2024

HscA is a Hsp70-type chaperone protein that plays an essential role to mediate the iron-sulfur (Fe-S) cluster biogenesis mechanism in Escherichia coli. Like other Hsp70 chaperones, HscA is composed of two domains: the nucleotide binding domain (NBD), which can hydrolyze ATP and use its chemical energy to facilitate the Fe-S cluster transfer process, and the substrate binding domain (SBD), which directly interacts with the substrate, IscU, the scaffold protein of an Fe-S cluster. In the present work, we prepared the isolated SBD construct of HscA (HscA(SBD)) and conducted the solution-state nuclear magnetic resonance (NMR) experiments to have its backbone chemical shift assignment information. Due to low spectral quality of HscA(SBD), we obtained all the NMR data from the sample containing the peptide LPPVKIHC, the HscA-interaction motif of IscU, from which the chemical shift assignment could be done successfully. We expect that this information provides an important basis to execute detailed structural characterization of HscA and appreciate its interaction with IscU.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.138-142
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• 2016

Replication Protein A (RPA) is the eukaryotic single-stranded DNA binding protein. It involves in DNA replication, repair, and damage response. Among three subunits, RPA70 has a protein-protein binding domain (RPA70N) at the N-terminal. It has known that the domain recruits several damage response proteins to the damaged site. Also, it is suggested that there are more candidates that interact with RPA70N. Even though several studies performed on the structural aspects of RPA70N and its ligand binding, the backbone assignments of RPA70N is not available in public. In this study, we present the backbone assignments of RPA70N.

• Journal of the military operations research society of Korea
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• v.26 no.1
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• pp.56-69
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• 2000

A frequency assignment problem on time division duplex system is considered. Republic of Korea Army (ROKA) has been establishing an infrastructure of tactical communication (SPIDER) system for next generation and it will be a core network structure of system. VHF system is the backbone network of SPIDER, that performs transmission of data such as voice, text and images. So, it is a significant problem finding the frequency assignment with no interference under very restricted resource environment. With a given arbitrary configuration of communications network, we find a feasible solution that guarantees communication without interference between sites and relay stations. We formulate a frequency assignment problem as an Integer Programming model, which has NP-hard complexity. To find the assignment results within a reasonable time, we take a genetic algorithm approach which represents the solution structure with available frequency order, and develop a genetic operation strategies. Computational result shows that the network configuration of SPIDER can be solved efficiently within a very short time.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.5 no.1
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• pp.68-82
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• 2011

Wireless mesh networks (WMNs) provide high-speed backbone networks without any wired cable. Many researchers have tried to increase network throughput by using multi-channel and multi-radio interfaces. A multi-radio multi-channel WMN requires channel assignment algorithm to decide the number of channels needed for each link. Since the channel assignment affects routing and interference directly, it is a critical component for enhancing network performance. However, the optimal channel assignment is known as a NP complete problem. For high performance, most of previous works assign channels in a centralized manner but they are limited in being applied for dynamic network environments. In this paper, we propose a simple flow estimation algorithm and a hybrid channel assignment algorithm. Our flow estimation algorithm obtains aggregated flow rate information between routers by packet sampling, thereby achieving high scalability. Our hybrid channel assignment algorithm initially assigns channels in a centralized manner first, and runs in a distributed manner to adjust channel assignment when notable traffic changes are detected. This approach provides high scalability and high performance compared with existing algorithms, and they are confirmed through extensive performance evaluations.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.40 no.10
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• pp.67-78
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• 2003

As optical network technology advances and high bandwidth Internet is demanded for the exponential growth of internet traffic volumes, the Dense-Wavelength Division Multiplexing (DWDM) networks have been widely accepted as a promising approach to the Next Generation Optical Internet (NGOI) backbone networks for nation wide or global coverage. Important issues in the NGOI based on DWDM networks are the Routing and Wavelength Assignment(RWA) problem and survivability. Especially, fault/attack detection, localization and recovery schemes in All Optical Transport Network(AOTN) is one of the most important issues because a short service disruption in DWDM networks carrying extremely high data rates causes loss of vast traffic volumes. In this paper, we suggest a fault/attack management model for NGOI through analyzing fault/attack vulnerability of various optical backbone network devices and propose fault/attack recovery procedure considering Extended-LMP(Link Management Protocol) and RSVP-TE+(Resource Reservation Protocol-Traffic Engineering) as control protocols in IP/GMPLS over DWDM.

• Journal of Korean Institute of Industrial Engineers
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• v.26 no.4
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• pp.296-305
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• 2000

Virtual wavelength path (VWP) is the optical path when a wavelength conversion is possible in a wavelength division multiplexing (WDM) network that is transmission infrastructure for the next generation high speed backbone networks. To achieve efficient design for VWP networks, we must consider VWP routing, wavelength assignment, and wavelength conversion while satisfying many technical constraints of the WDM networks. In this study we propose an integrated model for efficient VWP design in WDM networks. We also develope a 3-phase algorithm, each of which deals with routing, wavelength assignment and route and wavelength reassignment, respectively. In our computational experiments, phase 1 algorithm can solve the problem to the optimality for medium size test networks. Phase 2 algorithm is an efficient heuristic based on a reduced layered network and can give us an effective wavelength assignment. Finally, phase 3 algorithm reconfigure VWP routing and its wavelength assignment to concentrate wavelength conversion nodes in the suggested VWP network.