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

• The Korean Journal of Physiology and Pharmacology
• /
• v.17 no.6
• /
• pp.547-551
• /
• 2013

We recently reported a Philyra pisum lectin (PPL) that exerts mitogenic effects on human lymphocytes, and its molecular characterization. The present study provides a more detailed characterization of PPL based on the results from a monosaccharide analysis indicating that PPL is a glycoprotein, and circular dichroism spectra revealing its estimated ${\alpha}$-helix, ${\beta}$-sheet, ${\beta}$-turn, and random coil contents to be 14.0%, 39.6%, 15.8%, and 30.6%, respectively. These contents are quite similar to those of deglycosylated PPL, indicating that glycans do not affect its intact structure. The binding properties to different pathogen-associated molecular patterns were investigated with hemagglutination inhibition assays using lipoteichoic acid from Gram-positive bacteria, lipopolysaccharide from Gram-negative bacteria, and both mannan and ${\beta}$-1,3-glucan from fungi. PPL binds to lipoteichoic acids and mannan, but not to lipopolysaccharides or ${\beta}$-1,3-glucan. PPL exerted no significant antiproliferative effects against human breast or bladder cancer cells. These results indicate that PPL is a glycoprotein with a lipoteichoic acid or mannan-binding specificity and which contains low and high proportions of ${\alpha}$-helix and ${\beta}$-structures, respectively. These properties are inherent to the innate immune system of P. pisum and indicate that PPL could be involved in signal transmission into Gram-positive bacteria or fungi.

• Bulletin of the Korean Chemical Society
• /
• v.27 no.7
• /
• pp.1015-1019
• /
• 2006

The peptide with structural similarity to mammalian substance P (M-SP) has been isolated from extract of the body of the African lungfish, Protopterus dolloi, using the rectum of the newt as the bioassay system. The primary structure of the SP-related peptide was identified as Lys-Pro-Arg-Pro-Asp-Gln-Phe-Tyr-Gly-Leu-Met-NH2 (L-SP) and contained four substitutions ($Lys^{1}\rightarrow $ Arg, $Arg^{3}\rightarrow$ Lys, $Asp^{5}\rightarrow$ Gln, and $Tyr^{8}\rightarrow$ Phe) compared with M-SP; this structure is identical to that of the peptide isolated from the gut of the Australian lungfish. Circular dichroism spectra showed that L-SP had an unordered structure in the buffer solution and phospholipid bilayers. This peptide was found to have an excitatory effect on rectal muscle tissues of newt, quail, and fish. L-SP also had a more potent vasodilatory effect on the guinea-pig aorta than that of M-SP. The identification of the peptide provides evidence that SP family, hitherto confined to mammals, have a widespread occurrence in lungfish.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.8
• /
• pp.2508-2512
• /
• 2012

Cold shock proteins (CSPs) are a family of proteins induced at low temperatures. CSPs bind to single-stranded nucleic acids through the ribonucleoprotein 1 and 2 (RNP 1 and 2) binding motifs. CSPs play an essential role in cold adaptation by regulating transcription and translation via molecular chaperones. The solution nuclear magnetic resonance (NMR) or X-ray crystal structures of several CSPs from various microorganisms have been determined, but structural characteristics of psychrophilic CSPs have not been studied. Therefore, we optimized the purification process to obtain highly pure Lm-Csp and determined the three-dimensional structure model of Lm-Csp by comparative homology modeling using MODELLER on the basis of the solution NMR structure of Bs-CspB. Lm-Csp consists of a ${\beta}$-barrel structure, which includes antiparallel ${\beta}$ strands (G4-N10, F15-I18, V26-H29, A46-D50, and P58-Q64). The template protein, Bs-CspB, shares a similar ${\beta}$ sheet structure and an identical chain fold to Lm-Csp. However, the sheets in Lm-Csp were much shorter than those of Bs-CspB. The Lm-Csp side chains, E2 and R20 form a salt bridge, thus, stabilizing the Lm-Csp structure. To evaluate the contribution of this ionic interaction as well as that of the hydrophobic patch on protein stability, we investigated the secondary structures of wild type and mutant protein (W8, F15, and R20) of Lm-Csp using circular dichroism (CD) spectroscopy. The results showed that solvent-exposed aromatic side chains as well as residues participating in ionic interactions are very important for structural stability. Further studies on the three-dimensional structure and dynamics of Lm-Csp using NMR spectroscopy are required.

• Journal of the Korean Chemical Society
• /
• v.29 no.5
• /
• pp.490-495
• /
• 1985

Novel palladium (II) complexes, $[Pd((ieaa)_2-en)]$ and [PdCl((ieaa)-l-pn)] ($(ieaa)_2-en)]$ and (ieaa)-l-pn denote N,N'-ethylenebis(isonitrosoethylacetoacetate imine) and l-N-(2-aminopropyl)-isonitrosoethylacetoacetate imine, respectively), have been prepared. The palladium (II) complexes were characterized on the bases of the electronic absorption, circular dichroism (CD), $^{13}C$ NMR, infrared, and Raman spectra. The reaction of palladium(II) cliloride and isonitrosoethylacetoacetate (ieaa) with methylenediamine gives an $(ieaa)_2-en)]$ type Schiff base, while similar reaction using l-propylenediamine instead of ethylenediamine gives an (ieaa)-l-pn type Schiff base. The difference in formation is discussed from the stereochemical viewpoint of the diamine employed.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2015.08a
• /
• pp.66.1-66.1
• /
• 2015

Plasma medicine is an upcoming research area that has attracted the scientists to explore more deeply the utility of plasma. So, apart from the treating biomaterials and tissues with plasma, we have studied the effect of plasma with different feeding gases on modification of biomolecules. Additionally, we have checked the action of nanosecond pulsed plasma on the biomolecules. We have checked the plasma action on proteins ((Hemoglobin (Hb) Myoglobin (Mb) and lysoenzyme), calf thymus DNA and amino acids. The structural changes or structural modification of proteins and DNA have been studied using circular dichroism (CD), dynamic light scattering (DLS), gel electrophoresis, protein oxidation test, UV-vis spectroscopy and 1D NMR, while Liquid Chromatograph/Capillary Electrophoresis-Mass Spectrometer(LC/CE-MS) based qualitative bio-analysis have been used to study the modification of amino acids. We have also shown the effect of NaCl and ionic liquid on the formation of OH radicals using electron spin resonance and fluorescence techinques.

• BMB Reports
• /
• v.40 no.2
• /
• pp.163-171
• /
• 2007

Functional elements of the conserved helix 7 in the poreforming domain of the Bacillus thuringiensis Cry $\delta$- endotoxins have not yet been clearly identified. Here, we initially performed alanine substitutions of four highly conserved aromatic residues, $Trp^{243}$, $Phe^{246}$, $Tyr^{249}$ and $Phe^{264}$, in helix 7 of the Cry4Ba mosquito-larvicidal protein. All mutant toxins were overexpressed in Escherichia coli as 130-kDa protoxins at levels comparable to the wild-type. Bioassays against Stegomyia aegypti mosquito larvae revealed that only W243A, Y249A or F264A mutant toxins displayed a dramatic decrease in toxicity. Further mutagenic analysis showed that replacements with an aromatic residue particularly at $Tyr^{249}$ and $Phe^{264}$ still retained the high-level toxin activity. In addition, a nearly complete loss in larvicidal activity was found for Y249L/F264L or F264A/ Y249A double mutants, confirming the involvement in toxicity of both aromatic residues which face towards the same direction. Furthermore, the Y249L/F264L mutant was found to be structurally stable upon toxin solubilisation and trypsin digestion, albeit a small change in the circular dichroism spectrum. Altogether, the present study provides for the first time an insight into the highly conserved aromaticity of $Tyr^{249}$ and $Phe^{264}$ within helix 7 playing an important role in larvicidal activity of the Cry4Ba toxin.

• BMB Reports
• /
• v.40 no.2
• /
• pp.232-238
• /
• 2007

The p13 gene is uniquely present in Group II nucleopolyhedroviruses (NPVs) and some granuloviruses, but not in Group I NPVs. p13 gene was first described by our laboratory in Leucania separatamultiple nuclear polyhedrosis virus (Ls-p13) in 1995. However, the functions of Ls-P13 and of its homologues are unknown. When Ls-p13 was inserted into Autographa californica nucleopolyhedrovirus, a Group I NPV, polyhedra yield was inhibited. However, this inhibition was prevented when the leucine zipper-like domain of Ls-p13 was mutated. To determine the cause of this marked difference between Ls-P13 and leucine zipper mutated Ls-P13 (Ls-P13mL), oligomerization and secondary structure analyses were performed. High performance liquid chromatography and yeast two-hybrid assays indicated that neither Ls-P13 nor Ls-P13mL could form oligomers. Informatics and circular dichroism spectropolarimetry results further indicated marked secondary structural differences between Ls-P13 and Ls-P13mL. The LZLD of Ls-P13 has two extended heptad repeat units which form a hydrophobic surface, but it is short of a third hydrophobic heptad repeat unit for oligomerization. However, the mutated LZLD of Ls-P13mL lacks the above hydrophobic surface, and its secondary structure is markedly different. This difference in its secondary structure may explain why Ls-P13mL is unable to inhibit polyhedra yield.

• BMB Reports
• /
• v.39 no.3
• /
• pp.270-277
• /
• 2006

Helices 4 and 5 of the Bacillus thuringiensis Cry4Ba $\delta$-endotoxin have been shown to be important determinants for mosquito-larvicidal activity, likely being involved in membrane-pore formation. In this study, the Cry4Ba mutant protein containing an additional engineered tryptic cleavage site was used to produce the $\alpha4$-$\alpha5$ hairpin peptide by an efficient alternative strategy. Upon solubilization of toxin inclusions expressed in Escherichia coli and subsequent digestion with trypsin, the 130-kDa mutant protoxin was processed to protease-resistant fragments of ca. 47, 10 and 7 kDa. The 7-kDa fragment was identified as the $\alpha4$-loop-$\alpha5$ hairpin via N-terminal sequencing and mass spectrometry, and was successfully purified by size-exclusion FPLC and reversed-phase HPLC. Using circular dichroism spectroscopy, the 7-kDa peptide was found to exist predominantly as an $\alpha$-helical structure. Membrane perturbation studies by using fluorimetric calcein-release assays revealed that the 7-kDa helical hairpin is highly active against unilamellar liposomes compared with the 65-kDa activated full-length toxin. These results directly support the role of the $\alpha4$-loop-$\alpha5$ hairpin in membrane perturbation and pore formation of the full-length Cry4Ba toxin.

• Journal of Pharmaceutical Investigation
• /
• v.22 no.2
• /
• pp.97-104
• /
• 1992

The purpose of this study was (i) to determine whether protease inhibition by medium chain fatty acids such as sodium caprate, sodium caprylate and sodium laurate led to suppression of insulin proteolysis over a range of insulin concentrations and (ii) elucidate preventing effect of the enhancers on molecular self-association of insulin in pH 7.4 phosphate buffer isotonic solution. To this end, the rate of insulin proteolysis in nasal tissue supernatants of the albino rabbits was determined in the presence of $0.1{\sim}2%$ sodium caprylate, sodium caprate and sodium laurate at insulin concentrations ranging from $5\;to\;100\;{\mu}M$. At fatty acid salts concentration lower than 0.5%, insulin proteolysis was accelerated but the enhancers of high concentration (>1%) reduced the rate of insulin proteolysis. These effects were dependent upon insulin concentration and chain length of fatty acid salts. Circular dichroism spectra of insulin solutions were then determined. Monomer fraction of insulin was increased with increasing sodium caprate. Therefore, half-life decrease of insulin at low concentrations of the enhancers was attributed to deaggregation of insulin by the enhancers, increasing the proportion of monomers available for nasal proteolysis. And the increase of half-life at high concentration of the enhancers was attributed to inhibitory effect on protease rather than the effect of monomer fraction.