• Journal of Life Science
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• v.15 no.4 s.71
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• pp.633-640
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• 2005

The purified xylanase from Bacillus pumilus TX703 was modified with various chemical modifiers to determine the active sites of the enzyme. Treatment of the enzyme with group-specific reagents such as carbodiimide or N-bromosuccinimide resulted in complete loss of enzyme activity. These results assumed that these reagents reacted with glutamic acid or aspartic acid and tryptophan residues located at or near the active site. In each case, inactivation was performed by pseudo first-order kinetics. Inhibition of enzyme activity by carbodiimide and W-bromosuccinimide showed non-competitive and competitive inhibition type, respectively. Addition of xylan to the enzyme solution containing N-bromosuccinimide prevented the inactivation, indicating the presence of tryptophan at the substrate binding site. Analysis of kinetics for inactivation showed that the loss of enzyme activity was due to modification of two glutamic acid or aspartic acid residues and single tryptophan residue.

• Journal of the Korean Magnetic Resonance Society
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• v.9 no.2
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• pp.110-121
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• 2005

E.coli methionyl tRNA synthetase consist of 676 amino acids and plays a key role in initiation of protein synthesis. The native form of this enzyme is a homodimer, but the monomeric enzyme truncated approximately C-terminal 120 amino acids retains the full enzymatic activities. X-ray crystal structure of the active monomeric enzyme shows that it has two domains. The N-terminal domain is thought to be a binding site for acceptor stem of tRNA, ATP, and methionine. The C-terminal domain is mainly a-helical and makes an interaction with the anticodon of $tRNA^{Met}$. Especially it is suggested that the region of helix-loop-helix including the tryptophan residue at the position 461 may be the essential for the interaction with anticodon of $tRNA^{Met}$. In this work the structure and function of E. coli methionyl-tRNA synthetase was studied by spectroscopic method (NMR, CD, Fluorescence). The importance of tryptophan residue at the position 461 was investigated by fluorescence spectroscopy. Tryptophan 461 is expected to be an essential site for the interaction between E. coli methionyl-tRNA synthetase and E. coli $tRNA^{Met}$. Proton and heteonuclear 2-dimensional NMR spectroscopy were also used to elucidate the protein-tRNA interaction.

• Bulletin of the Korean Chemical Society
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• v.24 no.8
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• pp.1188-1192
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• 2003

In order to study the role of residue in the active site of glutathione S-transferase (GST), Tyr 108 residue in human GST P1-1 was replaced with alanine, phenylalanine and tryptophan by site-directed mutagenesis to obtain mutants Y108A, Y108F and Y108W. These three mutant enzymes were expressed in Escherichia coli and purified to electrophoretic homogeneity by affinity chromatography on immobilized GSH. The substitutions of Tyr108 significantly affected $K_m^{CDNB}$ and $K_m^{ETA}$, whereas scarcely affected $K_m^{GSH}$. The substitutions of Tyr108 also significantly affected $I_{50}$ of ETA, an electrophilic substrate-like compound. The effect of these substitutions on kinetic parameters and the response to inhibition suggests that tyrosine 108 in hGST P1-1 contributes to the binding of the electrophilic substrate and a major determinant in the binding of CDNB is the aromatic ring of Tyr108, not its hydroxyl group.

• Journal of Life Science
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• v.32 no.9
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• pp.729-733
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• 2022

Aggregation of normally soluble proteins can cause disease-related problems. Tryptophan synthase α-subunit (αTS) in E. coli adopts one of most popular structural scaffolds, the TIM barrel fold. Previous mutagenesis of the αTS gene resulted in many aggregation-prone mutant proteins. Here, Y173F (Tyr at residue 173 to Phe) substitution, which imparts increased stability, was tested for its ability to suppress aggregation of aggregation-prone mutant proteins (Y4C, S33L, P28L, P28S, G44S, D46N, P96L, and P96S). Aggregation was suppressed in all eight severe aggregate-forming mutants (all differing in their mutation positions), by the Y173F replacement. P28L αTS, which was available in pure form, was further analyzed and showed reduced secondary structure content, lower stability, and a looser structure with more exposed hydrophobic surface compared to the wild type protein. A double mutant P28L/Y173F protein showed almost no indication of these changes compared to the wild type protein. We hypothesized that Tyr at position 173 in αTS is positioned at the hydrophobic core and may serve to suppress the aggregation of this protein caused by other residues. Important residue (s) could be working widely in the prevention/suppression of protein aggregation.

• Microbiology and Biotechnology Letters
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• v.11 no.3
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• pp.155-161
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• 1983

The effects of ultraviolet light on bacteriophage f2 were investigated to determine the inactivation kinetics and its mechanism. The 260nm light showed a little higher inactivation rate than the one of 300 nm. In this work, our main concern was whether structural and/or conformational changes in the protein capsid could occur by UV irradiation. The inactivation for the first 20 minutes irradiation was rapid with a loss of about 4 logs and followed by a slower rate during the next 40 minutes with no survival noted in the samples irradiated for 90 minutes or longer. The structural change of the protein capsid was examined by optical spectroscopic techniques and electron microscopy. The absorption spectra of the UV irradiated phages showed no detectable differences in terms of the spectral shape and intensity from the control phage. However, the fluorescence emission spectroscopic data, i.e. 1) fluorescence quenching of tryptophan residues upon irradiation of 300 nm light, 2) enhancement of fluorescence emission of ANS (8-aniline-1-naphthalene sulfonate) bound to the intact phages compared to the one in the UV-treated phages, and 3) decrease of energy transfer efficiency from tryptophan to ANS in the UV-treated samples, presented remarkable differences between the intact and UV-treated phages. Such a structural alteration was also observed by electron microscopy The UV-treated phages appeared to be broken and empty capsids. Therefore, the inactivation of the bacteriophage f2 by UV irradiation is thought to be attributed to the structural change in the protein capsid as well as damage in the viral RNA by UV irradiation.

• Journal of Photoscience
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• v.11 no.1
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• pp.29-33
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• 2004

The mechanism of interaction of cyanocobalamin (CB) with bovine serum albumin (BSA) has been investigated by spectrofluorometric and circular dichroism methods. Association constant for the CB-BSA system showed that the interaction is non-covalent in nature. Binding studies in the presence of an hydrophobic probe, 8-anilino-l-naphthalene sulphonic acid, sodium salt (ANS) showed that there is hydrophobic interaction between CB and ANS and they do not share common sites in BSA. Stern-Volmer analysis of fluorescence quenching data showed that the fraction of fluorophore (protein) accessible to the quencher (CB) was close to unity indicating thereby that both tryptophan residues of BSA are involved in drug-protein interaction. The rate constant for quenching, greater than $10^{10}$ $M^{-1}$ $s^{-1}$, indicated that the drug binding site is in close proximity to tryptophan residue of BSA. Thermodynamic parameters obtained from data at different temperatures showed that the binding of CB to BSA involves hydrophobic bonds predominantly. Significant increase in concentration of free drug was observed for CB in presence of paracetamol. Circular dichroism studies revealed the change in helicity of BSA due to binding of CB to BSA.

• Molecules and Cells
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• v.39 no.3
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• pp.211-216
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• 2016

CYP107W1 from Streptomyces avermitilis is a cytochrome P450 enzyme involved in the biosynthesis of macrolide oligomycin A. A previous study reported that CYP107W1 regioselectively hydroxylated C12 of oligomycin C to produce oligomycin A, and the crystal structure of ligand free CYP107W1 was determined. Here, we analyzed the structural properties of the CYP107W1-oligomycin A complex and characterized the functional role of the Trp178 residue in CYP107W1. The crystal structure of the CYP107W1 complex with oligomycin A was determined at a resolution of $2.6{\AA}$. Oligomycin A is bound in the substrate access channel on the upper side of the prosthetic heme mainly by hydrophobic interactions. In particular, the Trp178 residue in the active site intercalates into the large macrolide ring, thereby guiding the substrate into the correct binding orientation for a productive P450 reaction. A Trp178 to Gly mutation resulted in the distortion of binding titration spectra with oligomycin A, whereas binding spectra with azoles were not affected. The Gly178 mutant's catalytic turnover number for the 12-hydroxylation reaction of oligomycin C was highly reduced. These results indicate that Trp178, located in the open pocket of the active site, may be a critical residue for the productive binding conformation of large macrolide substrates.

• Journal of Life Science
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• v.12 no.4
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• pp.464-468
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• 2002

Enzymatic activities and fluorescence spectroscopic properties of the double mutant proteins P96L/F139W, P96L/F258W and a triple mutant protein P96L/F139W/F258W of tryptophan synthase $\alpha$ subunit from Escherichia coli was examined to study tertiary and local structure changes around the tryptophan residues. The enzymatic activities of P96l./F139W and P96L/F258W were similar, but P96L/F139W/F258W had lower activity, as compared to wild type. The fluorescence intensities of double mutant, P96L/F139W and P96L/F258W, were decreased but that of a triple mutant, P96L/F139W/F258W, was increased when compared to wild type. The sum of the maximum fluorescence intensity (fluorescence intensity at the λ$_{max}$) for the double mutant proteins was not equal to the intensity seen in the triple mutant protein. The enzymatic activity and fluorescence data indicate that the replacement of Pro$^{96}$ longrightarrowLeu might affect on the stability of helix 8 and the loop located between strand 4 and helix4. The result suggests that the tertiary structure of triple mutant (P96L/F139W/F258W), being different from wild type, might have more compact residual structure at the vicinity of 139 and 258.8.

• Microbiology and Biotechnology Letters
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• v.20 no.5
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• pp.551-558
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• 1992

The extracellular endoinulase from Streptomyces sp. 556 was purified and characterized, The culture broth was fractionated by ammonium sulfate saturation followed by DEAE-cellulose column chromatography and 5ephadex G-200 gel filtration, The ultimately purified fraction revealed a single band in 7.5% polyacrylamide gel electropherogram. The purified enzyme showed the maximal activity at pH 5.5-6.0 and $50^{\circ}C$, but lost 93% of inulase activity after 30 min incubation at $55^{\circ}C$ . The essen.tial amino acid residue for catalytic activity appeared to be tryptophan. This endo inulase was activated by $Mn^{2+}$, whereas inactivated by $Ag^{+}$, $Hg^{+}$, $Cu^{2+}$, $Zn^{2+}$, $Fe^{3+}$ and $Mo^{6+}$ EDTA and 8-hydroxyquinoline inhibited the enzyme so that the enzyme was considered to be a metalloenzyme. The Km value for inulin was 0.287 mM, and no invertase or $\alpha$-glucosidase activity was found in the enzyme.

• Genomics & Informatics
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• v.21 no.3
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.