• BMB Reports
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• v.42 no.6
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• pp.373-379
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• 2009

5-Hydroxyuridine (5-OHU) is a major lesion of uridine and cytosine produced in RNA by various chemical oxidants. To elucidate its biochemical and biophysical effects on RNA replication, the site-specifically modified oligoribonucleotides containing 5-OHU were synthesized with C5-hydroxy-5'-ODMTr-2'-TBDMS-uridine phosphoramidite using automated solid phase synthesis. The base-pairing properties of nucleotides opposite 5-OHU in 24 mer oligoribonulcleotides with dNTP were studied using three reverse transcriptases (Super-$Script^{TM}II$-, AMV-, MMLV-RT) in cDNA synthesis. Adenine as well as guanine was incorporated preferentially by all reverse transcriptases. In the UV-melting temperature experiment, the results from the relative stabilities of the base pairs were A : 5-OHU > G : 5-OHU > T : 5-OHU $\approx$ C : 5-OHU. Circular Dichroism (CD) studies showed that DNA-RNA containing 5- OHU heteroduplexes exhibit a similar conformation between the A-type RNA and B-type DNA. These results suggest that 5- OHU from oxidative damage was mainly influenced by adenine mismatch.

• Proceedings of the Korean Vacuum Society Conference
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• 1999.07a
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• pp.168-168
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• 1999

Recently, Fe/Si multilayered films (MLF) have been a focus of interest due to the strong antiferromagnetic (AF) coupling observed in such kind of MLF originates from the same nature as in the metal/metal MLF. In particular, a question of whether the spacer layer in the Fe/Si MLF is metallic or semiconducting is of interest. In spite of various experimental techniques envolved in the study, the chemical composition and the properties of the interfacial regions in the MLF exhibiting the AF coupling is still questionable. The nature of the AF coupling and the interfacial properties of Fe/Si MLF are investigated in this study. A series of Fe/Si MLF with a fixed nominal thickness of Fe(3nm) and a variable thickness of Sk(1.0-2.2nm) were deposited by RF-sputtering onto glass substrates at room temperature. The atomic structures and the actual sublayer thicknesses of the Fe/Si MLF are investigated by using x-ray diffraction. The magnetic-field dependence of the equatorial Kerr effect clearly shows an appearance of the AF coupling between Fe sublayers at tsi = 1.5 - 1.8 nm. the drastic discrepancies between the experimental magnetooptical (MO) and optical properties, and based on the assumption of sharp interfaces between Fe and Si sublayers leads to a conclusion that pure si is absent in the AF-coupled Fe/Si MLF. Introducing in the model nonmagnetic semiconducting FeSi alloy layers between Fe and Si sublayers or as spacer between pure Fe sublayers only slightly improves the agreement between model and experiment. A reasonable agreement between experimental and simulated MO spectra was reached with using the fitted optical properties for the spacer with a typical metallic type of behavior. The results of the magnetic properties measured by vibrating sample magnetometer and magnetic circular dichroism are also analyzed in connection with the MO and optical properties.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.106-111
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• 2015

Helicobacter pylori (H. pylori) survives in acidic and fluctuating pH conditions of the stomach. The pH effect on H. pylori proteins is important for the advanced understanding of its evolution and viability, although this bacterium has the molecular machinery that neutralizes the acidic condition. HP1492 is known as a conserved NifU-like protein from H. pylori. NifU is a nitrogen fixation protein that mediates the transfer of iron-sulfur (Fe-S) cluster to iron-sulfur proteins like ferredoxin. Commonly, the monomeric reduced state of NifU can be converted to the dimeric oxidized state by intermolecular disulfide bond formation. Because it remains unclear that HP1492 actually behaves as known NifU protein, we first found that this protein can adopt both oxidized and reduced forms using size exclusion chromatography. Circular dichroism experiment showed that HP1492 is relatively well-structured at pH 6.5, compared to other pH conditions. On the basis of the backbone resonance assignment of HP1492, we further characterized the residues that are sensitive to pH using NMR spectroscopy. These residues showing large chemical shift changes could be mapped onto the secondary structure of the protein. Our results could provide the foundation for structural and biophysical studies on a wide spectrum of NifU proteins.

• Journal of Microbiology and Biotechnology
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• v.25 no.1
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• pp.33-43
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• 2015

GAM-1 and GAM-2, two themostable glucoamylases from Aspergillus niger B-30, possess different molecular masses, glycosylation, and thermal stability. In the present study, the effects of additives on the thermal inactivation of GAM-1 and GAM-2 were investigated. The half-lives of GAM-1 and GAM-2 at 70℃ were 45 and 216 min, respectively. Data obtained from fluorescence spectroscopy, circular dichroism spectroscopy, UV absorption spectroscopy, and dynamic light scattering demonstrated that during the thermal inactivation progress, combined with the loss of the helical structure and a majority of the tertiary structure, tryptophan residues were partially exposed and further led to glucoamylases aggregating. The thermal stability of GAM-1 and GAM-2 was largely improved in the presence of sorbitol and trehalose. Results from spectroscopy and Native-PAGE confirmed that sorbitol and trehalose maintained the native state of glucoamylases and prevented their thermal aggregation. The loss of hydrophobic bonding and helical structure was responsible for the decrease of glucoamylase activity. Additionally, sorbitol and trehalose significantly increased the substrate affinity and catalytic efficiency of the two glucoamylases. Our results display an insight into the thermal inactivation of glucoamylases and provide an important base for industrial applications of the thermally stable glucoamylases.

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.953-958
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• 2008

A novel anthraquinone diamino-bridged bis($\beta$ -cyclodextrin) 2 was synthesized. The inclusion complexation behaviors of the native $\beta$ -cyclodextrin 1 and the novel bis($\beta$ -cyclodextrin) 2 with guests, such as acridine red (AR), neutral red (NR), ammonium 8-anilino-1-naphthalenesulfonate (ANS), sodium 2-(p-toluidinyl) naphthalenesulfonate (TNS) and rhodamine B (RhB) were investigation by fluorescence, circular dichroism and 2D NMR spectroscopy. The spectral titrations were performed in phosphate buffer (pH 7.20) at 25 ${^{\circ}C}$ to give the complex stability constants (Ks) and Gibbs free energy changes (−${\Delta}G^0$) for the stoichiometric 1:1 inclusion complexation of host 1 and 2 with guests. The results indicated that the novel bis($\beta$ -cyclodextrin) 2 greatly enhanced the original binding affinity of the native $\beta$ -cyclodextrin 1. Typically, bis($\beta$ -cyclodextrin) 2 showed the highest binding constant towards ANS up to 34.8 times higher than that of 1. The 2D NMR spectra of bis($\beta$ -cyclodextrin) 2 with RhB and TNS were performed to confirm the binding mode. The increased binding affinity and molecular selectivity of guests by bis($\beta$ -cyclodextrin) 2 were discussed from the viewpoint of the size/shape-fit concept and multipoint recognition mechanism.

• Journal of Microbiology and Biotechnology
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• v.16 no.9
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• pp.1434-1440
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• 2006

The stable anchorage of pyridoxal 5'-phosphate (PLP) in the active site of D-amino acid transaminase (D-AT) is crucial for the enzyme catalysis. The three-dimensional structure of D-AT revealed that Glu32 is one of the active site groups that may playa role in PLP binding. To prove the role of Glu32 in PLP stability, we firstly checked the rate of the potential rate-limiting step. The kinetic analysis showed that the rate of the ${\alpha}$-deprotonation step reduced to 26-folds in E32A mutant enzyme. Spectral analyses of the reaction of D-AT with D-serine revealed that the E32A mutant enzyme failed to stabilize the key enzyme-substrate intermediate, namely a quinonoid intermediate (E-Q). Finally, analysis of circular dichroism (CD) on the wild-type and E32A mutant enzymes showed that the optical activity of PLP in the enzyme active site was lost by the removal of the carboxylic group, proving that Glu32 is indeed involved in the cofactor anchorage. The results suggested that the electrostatic interaction network through the groups from PLP, Glu32, His47, and Arg50, which was observed from the three-dimensional structure of the enzyme, plays a crucial role in the stable anchorage of the cofactor to give necessary torsion to the plane of the cofactor-substrate complex.

• Journal of Microbiology and Biotechnology
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• v.28 no.6
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• pp.987-996
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• 2018

Bacterial programmed cell death is regulated by the toxin-antitoxin (TA) system. YhaV (toxin) and Pr1F (antitoxin) have been recently identified as a type II TA system in Escherichia coli. YhaV homologs have conserved active residues within the C-terminus, and to characterize the function of this region, we purified native YhaV protein (without denaturing) and constructed YhaV proteins of varying lengths. Here, we report a new low-temperature method of purifying native YhaV, which is notable given the existing challenges of purifying this highly toxic protein. The secondary structures and thermostability of the purified native protein were characterized and no significant structural destruction was observed, suggesting that the observed inhibition of cell growth in vivo was not the result of structural protein damage. However, it has been reported that excessive levels of protein expression may result in protein misfolding and changes in cell growth and mRNA stability. To exclude this possibility, we used an [$^{35}S$]-methionine prokaryotic cell-free protein synthesis system in vitro in the presence of purified YhaV, and two C-terminal truncated forms of this protein (YhaV-L and YhaV-S). Our results suggest that the YhaV C-terminal region is essential for mRNA interferase activity, and the W143 or H154 residues may play an analogous role to Y87 of RelE.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.69-69
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• 2003

Human CD99 is a ubiquitous 32-kDa transmembrane protein encoded by the mic2 gene. The major cellular functions of CD99 protein are related to homotypic cell adhension, apoptosis, vesicular protein transport, and differentiation of thymocytes or T cells. Recently it has been reported that expression of a splice variant of CD99 transmembrane protein (Type I and Type II) increases invasive ability of human breast cancer cells. To understand structural basis for cellular functions of CD99 (Type I), we have initiated studies on hCD99$^{TMcytoI}$ and hCD99$^{cytoI}$ using circular dichroism (CD) and multi-dimensional NMR spectroscopy. CD spectrum of hCD99$^{TMcytoI}$ in the presence of 200mM DPC and CHAPS displayed an existence $\alpha$-helical conformation. The solution structure of hCD99$^{cytoI}$ determined by NMR is composed of one N-terminal $\alpha$-helix, $\alpha$A, two C-terminal short $\alpha$-helix segments, $\alpha$B and $\alpha$C. While $\alpha$A and $\alpha$B are connected by the long flexible loop, $\alpha$B and $\alpha$C connected by type III$\beta$-turn. Although it has been rarely figured out the correlation between structure and functional mechanism of hCD99$^{TMcytoI}$ and hCD99$^{cytoI}$, there is possibility of dimerization or oligomerization. In addition, the feasible mechanism of hCD99$^{cytoI}$ is that it could have intramolecular interaction between the N- and C- terminal domain through large flexible AB loop.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1479-1484
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• 2010

Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). Chlorophyll binding by the photosystem II subunit S protein, PsbS, was found to be necessary for energy-dependent quenching (qE), the major energy-dependent component of non-photochemical quenching (NPQ) in Arabidopsis thaliana. It is proposed that PsbS acts as a trigger of the conformational change that leads to the establishment of nonphotochemical quenching. However, the exact structure and function of PsbS in PSII are still unknown. Here, we clone and express the recombinant PsbS gene from Arabidopsis thaliana in E. coli and purify the resulting homogeneous protein. We used various biochemical and biophysical techniques to elucidate PsbS structure and function, including circular dichroism (CD), fluorescence, and DSC. The protein shows optimal stability at $4^{\circ}C$ and pH 7.5. The CD spectra of PsbS show that the conformational changes of the protein were strongly dependent on pH conditions. The CD curve for PsbS at pH 10.5 curve had the deepest negative peak and the peak of PsbS at pH 4.5 was the least negative. The fluorescence emission spectrum of the purified PsbS protein was also measured, and the ${\lambda}_{max}$ was found to be at 328 nm. PsbS revealed some structural changes under varying temperature and oxygen gas condition.

• Bulletin of the Korean Chemical Society
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• v.28 no.5
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• pp.730-736
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• 2007

The interaction of a polyoxometal (POM), K6SiW11Co(H2O)O39.10H2O (K6) as a Keggin, with human serum albumin (HSA) was studied by different methods and techniques. Binding studies show two sets of binding sites for interaction of POM to HSA. Binding analysis and isothermal calorimetery revealed that, the first set of binding site has lower number of bound ligand per mole of protein (ν), lower Hill constant (n), higher binding constant (K), more negative entropy (ΔS) and more electrostatic interaction in comparison to the second set of binding site. In addition, differential scanning calorimetery (DSC) and spectrophotometery data showed that, there are two energetic domains. The first domain is less stable (lower Tm and Cp) which corresponds to the tail segment of HSA and another with more stability is related to the head segment of HSA. Polyoxometal also decreases the stability of protein as Tm, secondary and tertiary structure as well as quenching of the fluorescence decrease. On other hand, perturbations in tertiary structure are more than secondary structure.