• Journal of the Korean Chemical Society
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• v.29 no.5
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• pp.552-554
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• 1985

• Analytical Science and Technology
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• v.8 no.3
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• pp.221-227
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• 1995

The fiber optic fluorosensor that shows a specific selectivity for calcium ion is studied. This sensor employs protein Calmodulin(CaM) which forms a fluorescent chelate with $Ca^{2+}$. A dialysis membrane is used to entrap a fluorescein isothiocyanate-labeled CaM solution at the common end of a bifurcated fiber optic bundle. The sensing mechanism of this sensor is based on the shifts in the fluorescence spectrum of metal-calmodulin complexes which FCaM forms a chelate with $Ca^{2+}$. Upon binding with $Ca^{2+}$, CaM undergoes a conformational change which induces a change in the fluorescence of FCaM. This change in fluorescence signal which is measured by photomultiflier tube is related to the concentration of $Ca^{2+}$ for calibration curve. Detection limit for $Ca^{2+}$ and the interference effects by $Mg^{2+}$, $Eu^{3+}$ and $La^{3+}$ for this sensor are studied. Response time and life time for this fluorosensor are also investigated.

• BMB Reports
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• v.40 no.5
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• pp.649-655
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• 2007

The nsp14 protein is an exoribonuclease that is encoded by severe acute respiratory syndrome coronavirus (SARS-CoV). We have cloned and expressed the nsp14 protein in Escherichia coli, and characterized the nature and the role(s) of the metal ions in the reaction chemistry. The purified recombinant nsp14 protein digested a 5'-labeled RNA molecule, but failed to digest the RNA substrate that is modified with fluorescein group at the 3'-hydroxyl group, suggesting a 3'-to-5' exoribonuclease activity. The exoribonuclease activity requires $Mg^{2+}$ as a cofactor. Isothermal titration calorimetry (ITC) analysis indicated a two-metal binding mode for divalent cations by nsp14. Endogenous tryptophan fluorescence and circular dichroism (CD) spectra measurements showed that there was a structural change of nsp14 when binding with metal ions. We propose that the conformational change induced by metal ions may be a prerequisite for catalytic activity by correctly positioning the side chains of the residues located in the active site of the enzyme.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1994.04a
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• pp.267-267
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• 1994

In order to obtain insight into the mechanism by which DNA containing a thymine photo-dimer is recognized by the excision repair enzyme, T$_4$ endonuclease V, we have taken NMR study of this protein and its complex with oligonucleotides. The conformations of five different DNA duplexes DNA I : d(GCGGATGGCG).d(CGCCTACCGC), DNA II d(GCGGTTGGCG) .d(CGCCAACCGC), DNA III : d(GCGGT ^ TGGCG) .d(CGCCAACCGC), DNA IV d(GCGGGCGGCG).d(CGCCCGCCGC) and DNA V d(GCGGCCGGCG) . d(CGCCGGCCGC) were studied by $^1$H NMR. The NMR spectra of these five DNA duplexes in the absence of the enzyme clearly show that the formation of a thymine dimer within the DNA induces only a minor distortion in the structure, and that the overall structure of B type DNA is retained. The photo-dimer formation is found to cause a large change in chemical shifts at the GC7 base pair, which is located at the 3'-side of the thymine dimer, accompanied by the major conformational change at the thymine dimer site. The binding of a mutant T$_4$ endonuclease V (E23Q), which is unable to digest DNA containing a thymine dimer, to the DNA duplex d(GCGGT ^ TGGCG)ㆍd(CGCCAACCGC) causes a large down-field shift in the imino proton resonance of GC7. Therefore, this position is thought to be either the crucial point of the interaction wi th T$_4$ endonuclease V, or the si to of a conformational change in the DNA caused by the binding of T$_4$ endonuclease V. Usually, it is very difficult to assign NMR peaks in DNA * protein complex because of severe peak overlaps. In order to overcome these peak overlaps, we used a method of deuterium incorporation.

• Bulletin of the Korean Chemical Society
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• v.32 no.9
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• pp.3433-3436
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• 2011

Some of metal nanoparticles have the potential for use as colorimetric assays for estimating solution properties, such as pH and temperature due to localized surface plasmon (LSP) phenomena. This report describes the use of silver nanoparticles (AgNP) conjugated with cytochrome c (Cyt c) for the colorimetric determination of solution pHs. When the pH of a solution decreases, the Cyt c immobilized on the AgNP undergoes a conformational change, leading to a decrease in the interparticle distance between Cyt c-AgNP probes and consequent red-shift in LSP. As a result, the color of the Cyt c-AgNP probe solution changes from yellow to red and finally to a grayish blue in the pH range from 11 to 3. This gradual color change can be used to determine the pH of a solution over a wide pH range, compared to other colorimetric methods that use gold nanoparticles.

• Journal of the Korean Magnetic Resonance Society
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• v.14 no.2
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• pp.127-133
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• 2010

Redox-dependent conformational change of human 8-kDa Dynein light chain (LC8) plays important role in regulating NF-${\kappa}B$ signaling pathway. In this study we characterized the structural states of the oxidized and reduced forms of LC8 by using NMR spectroscopy. The $^1H-^{15}N$ 2D HSQC spectra of oxidized LC8 indicated that no significant change in tertiary structure of LC8 occurred upon oxidation. The chemical shift perturbations of LC8 upon oxidation suggest a redox-dependent quaternary structural change.

• Molecules and Cells
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• v.27 no.6
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• pp.673-680
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• 2009

Conversion of the normal soluble form of prion protein, PrP ($PrP^C$), to proteinase K-resistant form ($PrP^{Sc}$) is a common molecular etiology of prion diseases. Proteinase K-resistance is attributed to a drastic conformational change from ${\alpha}$-helix to ${\beta}$-sheet and subsequent fibril formation. Compelling evidence suggests that membranes play a role in the conformational conversion of PrP. However, biophysical mechanisms underlying the conformational changes of PrP and membrane binding are still elusive. Recently, we demonstrated that the putative transmembrane domain (TMD; residues 111-135) of Syrian hamster PrP penetrates into the membrane upon the reduction of the conserved disulfide bond of PrP. To understand the mechanism underlying the membrane insertion of the TMD, here we explored changes in conformation and membrane binding abilities of PrP using wild type and cysteine-free mutant. We show that the reduction of the disulfide bond of PrP removes motional restriction of the TMD, which might, in turn, expose the TMD into solvent. The released TMD then penetrates into the membrane. We suggest that the disulfide bond regulates the membrane binding mode of PrP by controlling the motional freedom of the TMD.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• Bulletin of the Korean Chemical Society
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• v.16 no.2
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• pp.112-120
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• 1995

The conformational study on malonic acid, hydrogen malonate, malonate, malonyl methyl sulfide, and malonyl methyl sulfide anion, as the model compounds of malonyl-CoA, was carried out using the semiempirical MO methods (MNDO, AM1, and PM3) and hydration shell model. On the whole, the feasible conformations of malonic acid, hydrogen malonate, and malonate seem to be similar to each other. In malonic acid and malonate, two carboxyl groups are nearly perpendicular to the plane of the carbon skeleton, despite of different orientation of two carboxyl groups themselves. In particular, two carboxyl groups of hydrogen malonate are on the plane formed by carbon atoms with an intramolecular hydrogen bond. The calculated results on the geometry and conformation of three compounds are reasonably consistent with those of X-ray and spectroscopic experiments as well as the previous calculations. The orientation of two carbonyl groups of malonyl methyl sulfide is quite similar to that of malonic acid, but different from that of its anion. Especially, the computed probable conformations of the sulfide anion by the three methods are different from each other. The role of hydration seems not to be crucial in stabilizing the overall conformations of malonic acid, hydrogen malonate, malonate, and malonyl methyl sulfide. However, the probable conformations of the unhydrated sulfide anion obtained by the MNDO and AM1 methods become less stabilized by including hydration. The AM1 method seems to be appropriate for conformational study of malonyl-CoA and its model compounds because it does not result in the formation of too strong hydrogen bonds and significant change in conformational energy from one compound to another.

• Proceedings of the KOSOMBE Conference
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• v.1994 no.12
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• pp.187-189
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• 1994