• Journal of Integrative Natural Science
• /
• v.10 no.2
• /
• pp.105-109
• /
• 2017

Urotensin-2 receptor (UTS2R) is the most potent vasoconstrictor and plays a major role in the pathophysiology of various cardiovascular diseases and becomes a potential target for human pharmacotherapy. Hence, we have performed molecular docking of six antagonists with different inhibitory activity against UTS2R into its binding site. The binding mode of these antagonists was obtained using Surflex dock program interfaced in Sybyl-X2.0. The residues such as GLN278, THR304, TYR305, THR300, LEU299, CYS302, ASP47, TYR100 and THR304 are found in interaction between UTS2R and its antagonists. This study could be useful for identifying and analyzing the important residues involved in binding site of UTS2R receptor.

• Journal of the Korean Magnetic Resonance Society
• /
• v.16 no.1
• /
• pp.67-77
• /
• 2012

The small molecule binding to the c-Jun N-terminal kinase 3 (JNK3) was examined by the measurements of saturation transfer difference (STD) NMR experiments. The STD NMR experiment of ATP added to JNK3 clearly showed the binding of the nucleotide to the kinase. The STD NMR spectrum of dNTPs added to JNK3 discriminated the kinase-bound nucleotide from the unbound ones. After the five-fold addition of ATP to the dNTPs and JNK3 mixture, only signals of the cognate substrate of JNK3, ATP, were observed from the STD NMR experiment. These results signify that by the STD NMR the small molecules bound to JNK3 can be discriminated from the pool of the unbound molecules. Furthermore the binding mode of the small molecule to JNK3 can be determined by the competition experiments with ATP.

• Journal of the Korean Magnetic Resonance Society
• /
• v.2 no.1
• /
• pp.50-58
• /
• 1998

The systematic chirality investigations were made on the basic of the fact that zinc-binding tallysomycin (ZnTLMA) could have chiral centers (Zn, NC3, C6) at possible 4-, 5-, and 6-coordination models. Although our NMR data exhibit that the ligation sites are ${\beta}$-aminoalanine, ${\beta}$-hydroxyhistidine, and pyrimidine moiety, all possible coordination modes were tested out to see what kind of chiralities on NC3-C6 are favorable to each coordination mode. Tests were also made that take into account the specific configuration of functional groups, including ${\beta}$-aminoalanine, sugar ring, and ${\beta}$-hydroxyhistidine. Tests were finally extended to zinc-water binding and specific conformational studies by introducing various hydrogen bonding networks associated with the propionamide side chain and the carbamide group of mannose. Results of systematic chirality investigations exhibit that the S-S configuration of NC3-C6 is favorable to all of coordination models, but the R-S configuration, if exists at all, should have internal strain on C6 chiral center.

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

• Language and Information
• /
• v.6 no.2
• /
• pp.171-185
• /
• 2002

I claim that the asymmetry of locality effects in wh-questions involving Complex Noun Phrase Island in Korean follows from the proposal for the asymmetric mode of scope taking between way (why) and the other wh-words in Korean as laid out in Choi (2002). 1 will show that the present proposal is superio. to the LF pied-piping approach in Nishigauchi (1990) and WH-structure pied-piping in von Stechow(1996) in that it does not have the fatal problem of wrong semantics in Nishigauchi and Subjacency violation problem in von Stechow. The crossed reading in examples involving Wh-island has an interesting implication for the mechanism of unselective binding, suggesting that Heim's (1982) quantifier indexing mechanism, which requires the local unselective binding of the indefinite by the unselective binder, may be too strong.

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

• Interdisciplinary Bio Central
• /
• v.1 no.1
• /
• pp.3.1-3.6
• /
• 2009

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

• Bulletin of the Korean Chemical Society
• /
• v.29 no.8
• /
• pp.1533-1538
• /
• 2008

Porphyrins generally bind DNA in two different ways with respect to the mixing ratio; monomeric binding at a low mixing ratio and outside stacking at a high mixing ratio. In the present study, CTDNA binding property of a planar structured porphyrin, 5,10,15,20-tetrakis(N-methyl-4-pyridin-4-yl-phenyl)porphyrin (referred to as B-TMPyP) was investigated using absorption, CD, LD, and $LD^r$ spectroscopies. B-TMPyP produced a bisignate CD band, even at the lowest mixing ratio, indicating that B-TMPyP may not have a monomeric binding mode. From the observations of the spectral changes to the absorption, CD, and LD spectra in mixing ratio dependent titrations, B-TMPyP seems to have a quite different stacking type compared to that for the binding of $H_2$TMPyP. Moreover, B-TMPyP produced a CD band of opposite shape in the Soret band region. A qualitative explanation for the observed optical differences is also given.

• Journal of the Institute of Electronics Engineers of Korea TC
• /
• v.44 no.10
• /
• pp.148-155
• /
• 2007

The routing optimization mode, which Mobile IPv6 provides for the direct communication between a mobile node and its correspond node, introduces various security threats, thus causing several protocols to be proposed for the secure binding update procedure. In particular, the Kang-Park protocol, which Kang and Park presented in 2005, achieves the optimized cryptographic operations and the strong security, while based on its unique security proxy structure. In spite of such advantages, it has some drawbacks in terms of security and efficiency. This paper improves the Kang-Park protocol through the strong CoA validation and early binding update methods. Also, we show that the improved protocol is better than others.

• The korean journal of orthodontics
• /
• v.20 no.2
• /
• pp.409-417
• /
• 1990

Tooth movement would be impeded by frictional force arised between archwire and tube, bracket or elastics in the fixed orthodontic appliances, which could be changed variably by such several factors as the contact area, normal (perpendicular) force and the condition of contact surface. There were many literatures about frictional force in the orthodontic region, but different results were obtained from little controlled research so that was very difficult in clinical application. Therefore we have reviewed comprehensively previous literatures about frictional force and thus several results were obtained as follows: 1. For use species of the orthodontic wire, frictional force was influenced mainly by surface roughness of wire in the absence of binding, while that was influenced mainly by normal force in high binding angulation. 2. For the cross-section and diameter of the wire, the contact area influenced mainly on frictional force in the absence of binding, while wire stiffness influenced mainly on frictional force in high binding angulation. 3. The greater the bracket width, the greater frictional force, and frictional force of the plastic bracket was larger than that of the metal bracket. 4. For ligation type, frictional force of the stainless steel ligation was larger than that of the elastic ligation, and frictional force was directly proportional to ligation force. 5. Variable frictional force were occured from the saliva combined with such another factors as normal force and mode of surface oxide et al.