• Proceedings of the Microbiological Society of Korea Conference
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• 2001.11a
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• pp.97-101
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• 2001

The fusion between viral envelope and target cell membrane is a central step of viral infection, and the fusion proteins located at viral envelope mediate such process. Gp41 of HIV is one of the fusion proteins whose structure and mechanism of membrane fusion had been extensively studied. Functionally important motives of gp41 are the N-terminus fusion peptide, the coiled-coil and the membrane proximal C-peptide regions. The role of these regions during the fusion process had been thoroughly examined. Specially, insertion of the fusion peptide into membrane and conformational change of the coiled-coil and C-peptide regions are assumed to be critical for the fusion mechanism. In addition, the coiled-coil region has been shown to interact with membrane, and the C-peptide region regulates the interaction in a dose dependent manner. Furthermore, fusion defective mutations of the coiled-coil region dramatically changed its binding affinity to membrane. These results suggested that the membrane binding property of the coiled-coil region is important for the fusion activity of gp41, and such property could be modulated by the interaction with the C-peptide region.

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2201-2206
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• 2010

To improve the separation property and stability of metal chelate Cu(II) column, three new kinds of multidentate aminocarboxy silica columns with cation-exchange properties were synthesized using glutamic acid (Glu), glutamic acidbromoacetic acid (Glu-BAA), glutamic acid-bromosuccinic acid (Glu-BSUA) as ligands and silica gel as matrix. The standard proteins were separated with prepared chromatographic columns. The stationary phases exhibited the metal chelate property after fixing copper ion (II) on the synthesized multidentate ligand silica columns. The binding capacity of immobilized metal ion was related with the dentate number of multidentate ligands. Chromatographic behavior of proteins and the leakage of immobilized metal ion on multidentate chelate Cu(II) columns were affected by the dentate number of multidentate ligands and competitive elution system directly. The results showed that quinquedentate Glu-BSUA-Cu(II) column exhibited better chromatographic property and stability as compared with tridentate Glu-Cu(II) column, tetradentate Glu-BAA-Cu(II) column and commonly used IDA-Cu(II) column.

• Bulletin of the Korean Chemical Society
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• v.34 no.6
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• pp.1875-1878
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• 2013

• The KIPS Transactions:PartA
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• v.9A no.2
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• pp.241-248
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• 2002

With the structure of tilde-area computing system which Is specified by a researching team in Vrije University, Netherlands, lots of researchers and developers have been progressing the studies of global location and interconnection services of distributed objects existing in global sites. Most of them halve focused on binding services of only non-duplicated computational objects existing wide-area computing sites without any consideration of duplication problems. But all of objects existing on the earth rave the duplicated characteristics according to how to categorize their own names or properties. These objects with the same property can define as duplicated computational objects. Up to now, the existing naming or trading mechanism has not supported the binding services of duplicated objects, because of deficiency of independent location service. For this reason, we suggest a new model that can not only manages locations of duplicated objects In wide-area computing environments, but also provide minimum binding time by considering both the optimal selection of one of duplicated objects and load balance among distributed systems. Our model is functionally divided into 2 parts, one part to obtain an unique object handle of duplicated objects with same property as a naming and trading service, and the other to search one or more contact addresses by a node manager using a liven object handle, as a location service For location transparency, these services are independently executing each other. Based on our model, we described structure of wide-area integrated tree and algorithms for searching and updating contact address of distributed object on this tree. finally, we showed a federation structure that can globally bind distributed objects located on different regions from an arbitrary client object.

• Journal of KIISE:Information Networking
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• v.31 no.1
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• pp.27-36
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• 2004

Frequent occurrence of binding update messages may incur high overhead in Mobile IP supporting users mobility. Thus, it needs to develop algorithms to deal with the situation. In this paper, we propose new lifetime assignment schemes for dynamic binding update considering the locality property related with mobile node's movement. Each mobile node maintains a profile which is based on log containing useful information about its visiting subnets. That is, it determines dynamic binding update lifetime for currently visiting subnet by computing past mean resident time recorded in the profile. In addition, we note that the resident time depends on the time when each node enters a subnet and thus, we devise another lifetime assignment algorithm. Extensive experiments are made to compare our schemes with existing Mobile IPv6 where major facts for performance comparison are both the number of binding update messages and the number of binding request messages. From the results, we come to know that our schemes obtain highly considerable performance improvements in terms of communication cost by decreasing the number of those messages.

• Bulletin of the Korean Chemical Society
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• v.19 no.6
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• pp.628-634
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• 1998

The properties of the n-type impurities nitrogen and phosphorus in diamond have been investigated by means of electronic band structure calculations within the framework of the semiempirical extended Huckel tight-binding method. For diamond with the nitrogen and phosphorus substitutional impurities, calculated density of states shows the impurity level deep in the band gap. This property can be derived from the substantial <111> relaxation of the impurity and nearest-neighbor carbon atoms, which is associated with the population of an antibonding orbital between them. The passivated donor property of the P-vacancy complex which lies deep in the gap is also discussed.

• Ocean and Polar Research
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• v.33 no.2
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• pp.159-169
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• 2011

Antifreeze proteins (AFPs) have ice binding affinity, depress freezing temperature and inhibit ice recystallization which protect cellular membranes in polar organisms. Recent structural studies of antifreeze proteins have significantly expanded our understanding of the structure-function relationship and ice crystal growth inhibition. Although AFPs (Type I-IV AFP from fish, insect AFP and Plant AFP) have completely different fold and no sequence homology, they share a common feature of their surface area for ice binding property. The conserved ice-binding sites are relatively flat and hydrophobic. For example, Type I AFP has an amphipathic, single ${\alpha}$-helix and has regularly spaced Thr-Ala residues which make direct interaction with oxygen atoms of ice crystals. Unlike Type I AFP, Type II and III AFP are compact globular proteins that contain a flat ice-binding patch on the surface. Type II and Type III AFP show a remarkable structural similarity with the sugar binding lectin protein and C-terminal domain of sialic acid synthase, respectively. Type IV is assumed to form a four-helix bundle which has sequence similarity with apolipoprotein. The results of our modeling suggest an ice-binding induced structural change of Type IV AFP. Insect AFP has ${\beta}$-helical structure with a regular array of Thr-X-Thr motif. Threonine residues of each Thr-X-Thr motif fit well into the ice crystal lattice and provide a good surface-surface complementarity. This review focuses on the structural characteristics and details of the ice-binding mechanism of antifreeze proteins.

• Bulletin of the Korean Chemical Society
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• v.30 no.8
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• pp.1743-1748
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• 2009

Novel 2-aminothiazolinium based tripodal receptors were designed and synthesized. The binding property of these receptors toward various anions was investigated by the isothermal titration calorimetry (ITC) method. Receptor 4 recognized the acetate anion with 1:1 stoichiometry, whereas it bound the other oxoanions such as sulfate and phosphate in complex modes. By modifying the phenyl groups at the 4-position of the thiazoline rings of the tripodal receptor 4 to induce a mutual aromatic stacking interaction among the three ligands, receptor 10 showed totally different binding behavior, which gave rise to the 1:1 binding mode for the sulfate anion. This result was confirmed by ESI MS spectrometry.

• Bulletin of the Korean Chemical Society
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• v.18 no.5
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• pp.519-522
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• 1997

A series of new ligands having convergent dicarboxylic acid functions, based-upon Rebek's cleft-type ionophore, have been prepared and their ion binding properties were investigated by the competitive extraction and transport experiments. The main purpose of the modification was to increase the lipophilicity of the Rebek's ionophore, which was attempted by utilizing propyl analog of Kemp's triacid or by changing the bridging unit. Ionophores 5 and 6 were found to have a pronounced ion-binding property toward Ca2+ ion. The selectivity in competitive extraction of ionophore 5 at pH 9 for Ca2+ over Mg2+ and Sr2+ is 2.0 and 59.3, respectively. The selectivity in competitive transport of ionophore 5 for Ca2+ over Mg2+ and Sr2+ is 29.8 and 99.3, and that of ionophore 6 is 10.0 and 23.2, respectively.

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.