• Journal of Microbiology and Biotechnology
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• v.18 no.5
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• pp.845-851
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• 2008

TolC is an outer membrane porin protein and an essential component of drug efflux and type-I secretion systems in Gram-negative bacteria. TolC comprises a periplasmic $\alpha$-helical barrel domain and a membrane-embedded $\beta$-barrel domain. TdeA, a functional and structural homolog of TolC, is required for toxin and drug export in the pathogenic oral bacterium Actinobacillus actinomycetemcomitans. Here, we report the expression of the periplasmic domain of TdeA as a soluble protein by substitution of the membrane-embedded domain with short linkers, which enabled us to purify the protein in the absence of detergent. We confirmed the structural integrity of the TdeA periplasmic domain by size-exclusion chromatography, circular dichroism spectroscopy, and electron microscopy, which together showed that the periplasmic domain of the TolC protein family fold correctly on its own. We further demonstrated that the periplasmic domain of TdeA interacts with peptidoglycans of the bacterial cell wall, which supports the idea that completely folded TolC family proteins traverse the peptidoglycan layer to interact with inner membrane transporters.

• Macromolecular Research
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• v.16 no.6
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• pp.539-543
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• 2008

Many natural proteins self-assemble in complex ways, either to fulfill their biological function or introduce particular properties, such as high strength and toughness. We report the morphological transition in water from a spherical to rod-like shape of Bombyx mori silk fibroin by reducing the pH. Transmission electron microscopy, scanning electron microscopy, and dynamic light scattering were used to characterize the dilute solutions of silk fibroin in an aqueous environment, and provide direct visualization of the transformation of spherical micelles at pH 6.8 to nanofibrils at pH 4.8. This change in morphology occurred as a result of the stretching entropy due to the formation of $\beta$-sheets, which was analyzed using circular dichroism spectroscopy. This study demonstrates the self-assembly of silk fibroin as a function of pH.

• International Journal of Industrial Entomology and Biomaterials
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• v.42 no.2
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• pp.25-32
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• 2021

Mulberry fruit (Morus alba L.) contains phytochemicals, including 1-deoxynojirimycin, quercetin-glucoside, kaempferol-glucoside, and anthocyanins, which have antioxidant effects. In this study, mulberry fruit extract was prepared at various temperatures (25-100℃) and water/ethanol solvent concentrations (0%-100% ethanol). Fourier-transform infrared spectroscopy (FT-IR) and circular dichroism (CD) data indicated that the content of bioactive compounds such as polyphenols and flavonoids was lower in 100% ethanolic extracts than in 30%-50% ethanolic extracts. Radical scavenging activity determined using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-di-3-ethylbenzthiazoline sulfonic acid (ABTS) assays was highly correlated with polyphenol and flavonoid content. In conclusion, 30%-50% ethanolic extracts contained the highest contents of bioactive compounds and exhibited high levels of radical scavenging activity. These findings may inform the use of mulberry fruit extract as a functional food.

• Journal of Microbiology and Biotechnology
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• v.30 no.12
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• pp.1810-1818
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• 2020

Inhibitor K562 (IK) protein was first isolated from the culture medium of K562 cells, a leukemia cell line, and is an inhibitory regulator of interferon-γ-induced major histocompatibility complex class II expression. Recently, exogenous truncated IK (tIK) protein showed potential as a therapeutic agent for inflammation-related diseases. In this study, we designed a novel putative anti-inflammatory peptide derived from tIK protein based on homology modeling of the human interleukin-10 (hIL-10) structure, and investigated whether the peptide exerted inhibitory effects against pro-inflammatory cytokines such as IL-17 and tumor necrosis factor-α (TNF-α). The peptide contains key residues involved in binding hIL-10 to the IL-10 receptor, and exerted strong inhibitory effects on IL-17 (43.8%) and TNF-α (50.7%). In addition, we used circular dichroism spectroscopy to confirm that the peptide is usually present in a random coil configuration in aqueous solution. In terms of toxicity, the peptide was found to be biologically safe. The mechanisms by which the short peptide derived from human tIK protein exerts inhibitory effects against IL-17 and TNF-α should be explored further. We also evaluated the feasibility of using this novel peptide in skincare products.

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

• Bulletin of the Korean Chemical Society
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• v.27 no.11
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• pp.1801-1808
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• 2006

The interaction between whey carrier protein $\beta$-lactoglobulin type A and B (BLG-A and -B) and 2,2'-bipyridin n-hexyl dithiocarbamato Pd(II) nitrate (BPHDC-Pd(II)), a new heavy metal complex designed for anticancer property, was investigated by fluorescence spectroscopy combined with chemometry and circular dichroism (CD) techniques. A strong fluorescence quenching reaction of BPHDC-Pd(II) to BLG-A and -B was observed. Hence, BPHDC-Pd(II) complex can be bound to both BLG-A and -B, and quench the fluorescence spectra of the proteins. The quenching constant was determined using the modified Stern-Volmer equation. The binding parameters were evaluated by fluorescence quenching method. The results of binding study provided evidences presence of two and three sets of binding sites on the BLG-B and -A, respectively, for BPHDC-Pd(II) complex. Using fluorescence spectroscopy and chemometry, the ability of BLG-A and -B to form an intermediate upon interaction with BPHDC-Pd(II) complex was assessed. CD studies displayed that under influence of different concentrations of BPHDC-Pd(II) complex, the regular secondary structure of BLG-B had no significant changes, whereas for BLG-A a transition from $\alpha$-helix to $\beta$-structure was appeared. The results for both of BLG-A and -B displayed that BPHDC-Pd(II) complex can induce a conformational transition from the native form to an intermediate state with a slightly opened conformation, which is detectable with chemometry analyses.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.176.2-176.2
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• 2013

Property of optical diagnostics for pulse-discharged plasma in liquid and its biological applications to proteins are investigated by making use of high voltage Marx generator. The Marx generator has been consisted of 5 stages, where each charging capacitor is 0.5 ${\mu}F$, to generate a high voltage pulse with rising time of $1{\mu}s$. We have applied an input voltage of 6 kV to the each capacitor of 0.5 ${\mu}F$. High voltage pulsed plasma has been generated inside a polycarbonate tube by a single-shot operation, where the breakdown voltage is measured to be 7 kV, current of 1.2 kA, and pulse width of ~ 1 ${\mu}s$ between the two electrodes of anode-cathode whose material is made of tungsten pin, which are immersed into the liquids. We have investigated the emitted hydrogen lines for optical diagnostics of high voltage pulsed plasma. The emission line of 656.3 nm from $H-{\alpha}$ and 486.1 nm from $H-{\beta}$ have been measured by a monochromator. If we assumed that the focused plasma regions satisfy the local thermodynamic equilibrium conditions, the electron temperature and density of the high voltage pulsed plasma in liquid could be obtained by the Stark broadening of optical emission spectroscopy. For the investigation of the influence of pulsed plasma on biological proteins, we have exposed it onto the proteins such as hemoglobin and myoglobin. The structural changes in these proteins and their analysis have also been obtained by circular dichroism (CD) and ultraviolet (UV) visible spectroscopy.

• 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.

• Journal of the Korean Magnetics Society
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• v.26 no.4
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• pp.124-128
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• 2016

We have investigated the electronic structures of intermetallic multilayer (ML) films of [$Co(2{\AA})/Pd(x{\AA})$] (x: the thickness of the Pd sublayer; x = $1{\AA}$, $3{\AA}$, $5{\AA}$, $7{\AA}$, $9{\AA}$) by employing soft X-ray absorption spectroscopy (XAS) and soft X-ray magnetic circular dichroism (XMCD). Both Co 2p XAS and XMCD spectra are found to be similar to one another, as well as to those of Co metal, providing evidence for the metallic bonding of Co ions in [Co/Pd] ML films. By analyzing the measured Co 2p XMCD spectra, we have determined the orbital magnetic moments and the spin magnetic moments of Co ions in [$Co(2{\AA})/Pd(x{\AA})$] ML films. Based on this analysis, we have found that the orbital magnetic moments are enhanced greatly when x increases from $1{\AA}$ to $3{\AA}$, and then do not change much for $x{\geq}3{\AA}$. This finding suggests that the interface spin-orbit coupling plays an important role in determining the perpendicular magnetic anisotropy in [Co/Pd] ML films.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.2117-2124
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• 2013

The binding properties and sequence selectivities of ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ (bip = 4,4'-biphenylene (imidazo [4,4-f][1,10]phenanthroline) complexes with $poly[d(A-T)_2]$ and $poly[d(G-C)_2]$ were investigated using conventional spectroscopic methods. When bound to $poly[d(A-T)_2]$, a large positive circular dichroism (CD) spectrum was induced in absorption region of the bridging moiety for both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes, which suggested that the bridging moiety sits in the minor groove of the polynucleotide. As luminescence intensity increased, decay times became longer and complexes were well-protected from the negatively charged iodide quencher compared to that in the absence of $poly[d(A-T)_2]$. These luminescence measurements indicated that Ru(II) enantiomers were in a less polar environment compared to that in water and supported by minor groove binding. An angle of $45^{\circ}$ between the molecular plane of the bridging moiety of the ${\Delta}{\Delta}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex and the local DNA helix axis calculated from reduced linear dichroism ($LD^r$) spectrum further supported the minor groove binding mode. In the case of ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex, this angle was $55^{\circ}$, suggesting a tilt of DNA stem near the binding site and bridging moiety sit in the minor groove of the $poly[d(A-T)_2]$. In contrast, neither ${\Delta}{\Delta}$-nor ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex produced significant CD or $LD^r$ signal in the absorption region of the bridging moiety. Luminescence measurements revealed that both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes were partially accessible to the $I^-$ quencher. Furthermore, decay times became shorter when bis-Ru(II) complexes bound to $poly[d(G-C)_2]$. These observations suggest that both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes bind at the surface of $poly[d(G-C)_2]$, probably electrostatically to phosphate group. The results indicate that ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ are able to discriminate between AT and GC base pairs.