• BMB Reports
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• v.39 no.2
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• pp.167-170
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• 2006

Bovine adenosine deaminase undergoes a nondenaturational conformational change at $29^{\circ}C$ upon heating which is characterized by a large increase in heat capacity. We have determined the transition state thermodynamics of the conformational change using a novel application of differential scanning calorimetry (DSC) which employs very slow scan rates. DSC scans at the conventional, and arbitrary, scan rate of $1^{\circ}C/min$ show no evidence of the transition. Scan rates from 0.030 to $0.20^{\circ}C/min$ reveal the transition indicating it is under kinetic control. The transition temperature $T_t$ and the transition temperature interval ${\Delta}T$ increase with scan rate. A first order rate constant $k_1$ is calculated at each $T_t$ from $k_1\;=\;r_{scan}/{\Delta}T$, where $r_{scan}$ is the scan rate, and an Arrhenius plot is constructed. Standard transition state analysis reveals an activation free energy ${\Delta}G^{\neq}$ of 88.1 kJ/mole and suggests that the conformational change has an unfolding quality that appears to be on the direct path to the physiological-temperature conformer.

• Bulletin of the Korean Chemical Society
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• v.3 no.2
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• pp.60-66
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• 1982

In relation to denaturation of proteins, thermally induced conformational change of poly(D-glutamic acid) was studied in the presence of poly(vinyl alcohol) at low pH, where poly(D-glutamic acid) undergoes a helix-to-${\beta}$ transition without any other polymer. In a dilute solution, poly(vinyl alcohol) enhanced the ${\alpah}-to-{\beta}_1$ transition of poly(D-glutamic acid) due to intermolecular interaction between the two polymers. On the other hand, this conformational change was interrupted to a large extent in a concentrated solution, due to the interpenetration of poly(vinyl alcohol) chain into poly(D-glutamic acid) chain which prevented the intramolecular association of poly(D-glutamic acid) chain. A conformational change from ${\beta}_1\;to\;{\beta}_2$ of poly(D-glutamic acid) was observed for the films obtained by casting during annealing the mixture solutions. The ${\beta}_2$ content in the cast film increased with increasing poly(vinyl alcohol) content in the mixture.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.770-774
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• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Bulletin of the Korean Chemical Society
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• v.4 no.3
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• pp.133-139
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• 1983

To understand the importance of Y-base adjacent to the anticodon stabilizing codon-anticodon interaction, a study has been undertaken for the model compound involving the interaction between Y-base and anticodon as well as the participation of water molecule by calculating the conformational free energy using an empirical potential function. We restrict our analysis to sites directly associated with Y-base by varying only the backbone torsion angles of Y-base. The hydration and $Mg^{+2}$ binding effects on the conformational stability of Y-base are calculated and discussed. The free Y-base is proved to be less stable than the hydrated one. The free energy change due to the hydration of Y-base amounts to -119.5 kcal/mole, in which the conformational energy change is -142.4 kcal/mole and the configurational entropy change is -76.9 e. u. It is found that the water molecules bound to Y-base and $Mg^{+2}$ contribute to the conformation of Y-base dominantly.

• Journal of Sensor Science and Technology
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• v.19 no.3
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• pp.214-220
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• 2010

Three-dimensional(3D) structure of specific DNA can be changed between two conformations under an external environmental transition such as pH and salt concentration variations. We have experimentally observed the conformational transitions of i-motif DNA using AFM cantilever bioassay. It is shown that pH change of a solvent induces the bending defleciton change of a cantilever functionalized by i-motif DNA. This indicates that cantilever bioassay enables the label-free detection of DNA structural changes upon pH change. It is implied that cantilever bioassay can be a de novo route to quantitatively understand the conformational transitions of biological molecules under environmental changes.

• Molecules and Cells
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• v.27 no.6
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• pp.681-687
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• 2009

We examined the effects of synthetic signal peptides, wild-type (WT) and export-defective mutant (MT) of ribose-binding protein, on the conformational changes of signal recognition particle 54 homologue (Ffh) in Escherichia coli. Upon interaction of Ffh with WT peptide, the intrinsic Tyr fluorescence, the transition temperature of thermal unfolding, and the GTPase activity of Ffh decreased in a peptide concentration-dependent manner, while the emission intensity of 8-anilinonaphthalene-1-sulfonic acid increased. In contrast, the secondary structure of the protein was not affected. Additionally, polarization of fluorescein-labeled WT increased upon association with Ffh. These results suggest that WT peptide induces the unfolded states of Ffh. The WT-mediated conformational change of Ffh was also revealed to be important in the interaction between SecA and Ffh. However, MT had marginal effect on these conformational changes suggesting that the in vivo functionality of signal peptide is important in the interaction with Ffh and concomitant structural change of the protein.

• BMB Reports
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• v.31 no.3
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• pp.227-232
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• 1998

The leukocyte NADPH oxidase of neutrophils is a membrane-bound enzyme that catalyzes the production of $O_2^-$ from oxygen using NADPH as an electron donor. Dormant in resting neutrophils, the enzyme acquires catalytic activity when the cells are exposed to appropriate stimuli. During activation, the cytosolic oxidase components $p47^{phox}$ and $p67^{phox}$ migrate to the plasma membrane, where they associate with cytochrome $b_{558}$, a membrane-bound flavohemoprotein, to assemble the active oxidase. The oxidase can be activated in a cell-free system; the activating agent usually employed is an anionic amphiphile such as sodium dodecyl sulfate (SDS). Because $p47^{phox}$ can translocate by itself during activation, the conformational change in $p47^{phox}$ may be responsible for the activation of NADPH oxidase. We show here that the treatment of $p47^{phox}$ with SDS leads to an increase in the reactivity of the sutbydryl group of cysteines toward N-ethylmaleimide, indicating that the conformational change occurs when $p47^{phox}$ is exposed to SDS. We propose that this change in conformation results in the appearance of a binding site through which $p47^{phox}$ interacts with cytochrome $b_{558}$during the activation process.

• Bulletin of the Korean Chemical Society
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• v.23 no.5
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• pp.776-778
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• 2002

• Bulletin of the Korean Chemical Society
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• v.32 no.10
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• pp.3553-3554
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• 2011

• YAKHAK HOEJI
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• v.36 no.6
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• pp.518-528
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• 1992

To determine the optimal conformation of sulfonylureas, the correlation between conformation and hypoglycemic activity of the two sulfonylureas of tolbutamide and chlorpropamide as hypoglycemic agent was studied using an empirical potential function (ECEPP/2) and the hydration shell model in the unhydrated and hydrated states. The conformational energy was minimized from several starting conformations with possible torsion angles in each molecule. The conformational entropy change of each conformation was computed using a harmonic approximation. To understand the hydration effect on the conformation of the molecules in aqueous solution, the contribution of water-accessible volume of each group or atom in the lowest-free-energy conformation was calculated and compared each other. From comparison of the computed lowest-free-energy conformations of two sulfonylureas, it could be suggested that the hydration of sulfonylurea moiety is related to increase the hypoglycemic activity. From the calculation results, it was known that the conformational entropy is the major contribution to stabilize the low-free-energy conformations of two sulfonylureas in unhydrated state. Whereas, in hydrated state, the hydration free energy largely contributes to the total free energies of low-free-energy conformations of tolbutamide and conformational entropy contributes to stabilize the low-free-energy conformations of chlorpropamide. The torsion angles from phenyl ring to urea moiety of the low-free-energy conformations of the two sulfonylureas were shown the nearly regular trend. On the basis of these results, the conformation exhibiting the optimal hypoglycemic activity of sulfonylureas and the binding direction to pancreatic receptor site A could be predicted. Also, according to the side chain lengthening of urea moiety, tolbutamide showed various conformational change. Therefore, steric effect may be important factor in the interaction between sulfonylureas and the putative pancreatic receptor.