• Bulletin of the Korean Chemical Society
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• 제33권9호
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• pp.3017-3024
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• 2012

The geometrical parameters, vibrational frequencies, and binding energies for $(H_2O_3)_n$ (n = 1-5) have been investigated using various quantum mechanical techniques. The possible structures of the clusters (n = 2-5) are fully optimized and the binding energies are predicted using energy differences at each optimized geometry. The harmonic vibrational frequencies are also determined and zero-point vibrational energies (ZPVEs) are considered for the better prediction of the binding energy. The best estimation of the binding energy for the dimer is 8.65 kcal/mol. For n = 2 and 3, linear structures with all trans forms of the HOOOH monomers are predicted to be the lowest conformations in energy, while the cyclic structures with all cis-HOOOH monomers are preferable structures for n = 4 and 5.

• 대한화학회지
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• 제58권2호
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• pp.153-159
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• 2014

Herein, the cyclic voltammetric (CV) investigations of structurally similar bisnitrocompounds (N3, N4, N5, N6, having different-$CH_2$-spacer length) is presented. CV study offered interesting interactional possibilities of bisnitrocompounds with chicken blood ds.DNA at physiological pH 4.7 and human body temperature, 310 K. The results indicated strong interaction by these symmetric molecules with ds.DNA and strength of binding is found to depend on length of $CH_2$ spacer group in their molecular structure. Thermodynamics derived from electrochemical binding parameters also favored the irreversible interactions. Moreover, threading intercalation mode of binding is suggested based on thermodynamic and kinetic binding parameters extracted from CV studies.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.221-227
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• 2005

THEMATICS is a simple computational method for predicting functional sites in proteins. The method computes the theoretical titration curves of the ionizable residues of a protein using its 3D structure, determines the residues with perturbed, non-Henderson-Hasselbalch titration behavior, and identifies clusters of these perturbed residues in physical proximity. We have shown previously that this method is highly successful in predicting catalytic sites in enzymes. In the present study, we apply the method to non-catalytic ligand-binding proteins. It is shown that THEMATICS can predict non-catalytic binding sites. The success rate is better than 80 % for a set of 30 non-catalytic, ligand-binding proteins. The application of the method to Glutamine-binding protein from E. coli is discussed in detail.

• Bulletin of the Korean Chemical Society
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• 제23권2호
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• pp.262-266
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• 2002

Computations are presented for the ortho- and para-substituted benzyl alcohol-$H_2O$ clusters. A variety of conformers are predicted, and their relative energies are compared. Binding energies of the clusters are computed, and detailed analysis is presented on the effects of substitution on the strength of the hydrogen bond in the clusters. F- and $NH_2-$ substituted clusters are studied to analyze the effects of electron-withdrawing and electron-pushing groups. In para-substituted clusters, the inductive effects are dominant, affecting the binding energies in opposite way depending on whether the hydroxyl group is proton-donating or -accepting. For ortho-substituted clusters, more direct involvement of the substituting group and the resulting geometry change of the hydrogen bond should be invoked to elucidate complicated pattern of the binding energy of the clusters.

• Bulletin of the Korean Chemical Society
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• 제35권7호
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• pp.2114-2122
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• 2014

The association of silybin with ${\beta}$-cyclodextrin and its influence on silybin's binding with bovine serum albumin are reported. The stoichiometry, binding constant, and the structure of silybin-${\beta}$-cyclodextrin inclusion complex are reported. The titrations of silybin with bovine serum albumin in the absence and presence of ${\beta}$-cyclodextrin are carried out and the differences in binding strengths are discussed. Molecular modeling is used to optimize the sites and mode of binding of silybin with bovine serum albumin. F$\ddot{o}$rster resonance energy transfer is calculated and the proximity of interacting molecules is reported in the presence and absence of ${\beta}$-cyclodextrin.

• Bulletin of the Korean Chemical Society
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• 제31권11호
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• pp.3291-3296
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• 2010

A gelastatins (1), natural MMP inhibitors, and their hydroxamate analogues (2) in TACE enzyme evaluated for discovery of potent TACE inhibitors. We have employed molecular dynamics simulations to compute the relative free energy of hydration and binding to TACE for gelastatin (1) and its hydroxamate analogue (2). The relative free energy difference is directly described in this article using the free energy perturbation approach as a means to accurately predict the TACE inhibitor of gelastatin analogues. The results show that the good agreement between the experimental and theoretical relative free energies of binding, gelastatin hydroxamate (2) binds stronger to TACE by -3.37 kcal/mol. The desolvation energy costs significantly reduced binding affinity, hydroxamate group associated with high desolvation energy formed strong favorable interactions with TACE with more than compensated for the solvation costs and therefore led to an improvement in relative binding affinity.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.305-308
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• 2008

We performed coupled-cluster calculations to determine the intermolecular interaction energy between two TiAu4 clusters. Our ab initio calculations predict that the binding energy is 2.89 eV, which is somewhat larger than the known binding energy of 2.0 eV for TiH4-TiH4. The intermolecular binding energy is relatively high, despite TiAu4 having all the attributes of a magic cluster. The favorable orbital interaction between occupied Au(6s) and unoccupied Ti(3d) orbitals leads to the strong dimeric interaction for TiAu4-TiAu4.

• Bulletin of the Korean Chemical Society
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• 제33권11호
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• pp.3788-3792
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• 2012

Spherical-shape melanin nanoparticles with good water-dispersibility were successfully synthesized by a simple oxidation polymerization of 3,4-dihydroxy-phenylalanin (DOPA) with $KMnO_4$. Similar features to those known from natural and synthetic melanin polymers were observed from prepared melanin nanoparticles by FT-IR, UV-Vis., and ESR spectroscopic methods. Their binding ability with several heavy metal ions from aqueous solution was quantitatively investigated, and the maximum binding capacities with melanin nanoparticles to lead, copper, and cadmium ions were obtained as 2.45, 2.17 and 1.88 mmol/g, respectively, which are much larger values than those reported from natural and synthetic melanin polymers. The large binding capacity and fast binding rate of melanin nanoparticles to metal ions can make them an excellent candidate for the remediation of contaminated water.

• BMB Reports
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• 제37권2호
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• pp.260-267
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• 2004

Transducin (T), the heterotrimeric guanine nucleotide binding protein in rod outer segments, serves as an intermediary between the receptor protein, rhodopsin, and the effector protein, cGMP phosphodiesterase. Labeling of T with dansyl chloride (DnsCl) inhibited its light-dependent guanine nucleotide binding activity. Conversely, DnsCl had no effect on the functionality of rhodopsin. Approximately 2-3 mol of DnsCl were incorporated per mole of T. Since fluoroaluminate was capable of activating DnsCl-modified T, this lysine-specific labeling compound did not affect the guanine nucleotide-binding pocket of T. However, the labeling of T with DnsCl hindered its binding to photoexcited rhodopsin, as shown by sedimentation experiments. Additionally, rhodopsin completely protected against the DnsCl inactivation of T. These results demonstrated the existence of functional lysines on T that are located in the proximity of the interaction site with the photoreceptor protein.

• Bulletin of the Korean Chemical Society
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• 제30권11호
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• pp.2717-2722
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• 2009

The use of the classification and regression tree (CART) methodology was studied in a quantitative structure-activity relationship (QSAR) context on a data set consisting of the binding affinities of 39 imidazobenzodiazepines for the α1 benzodiazepine receptor. The 3-D structures of these compounds were optimized using HyperChem software with semiempirical AM1 optimization method. After optimization a set of 1481 zero-to three-dimentional descriptors was calculated for each molecule in the data set. The response (dependent variable) in the tree model consisted of the binding affinities of drugs. Three descriptors (two topological and one 3D-Morse descriptors) were applied in the final tree structure to describe the binding affinities. The mean relative error percent for the data set is 3.20%, compared with a previous model with mean relative error percent of 6.63%. To evaluate the predictive power of CART cross validation method was also performed.