• Bulletin of the Korean Chemical Society
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• v.20 no.10
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• pp.1159-1164
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• 1999

The study investigated the effect of carrier composition (ionic strength and pH) on the retention of various proteins in flow field-flow fractionation (Flow FFF) as well as the conformational change of Bovine Serum Albumin (BSA) with urea concentration, storage time and temperature. The study found that the retention of protein in Flow FFF increased with the ionic strength of the carrier liquid. Most proteins were well solubilized at pH = 7-8. The hydrodynamic diameters obtained from Flow FFF retention data agree well with theoretical values. The retention increased and the peak shape became distorted at extreme pH conditions of the carrier solution. The selected carrier composition for comparison between the literature value of proteins was 0.05 M tris buffer solution with a pH of 8. Storing BSA at 4 ±2℃ over a period of three months resulted in slow dimerization. Also, in case of the storage of BSA at 37 ±5℃ for one week, the retention of both BSA monomer and dimer increased with the urea concentration. Finally, the structural composition of specific enzymes: malonyl-CoA decarboxylase (MCDC) and malonyl-CoA synthesis (MCS) was determined by using Flow FFF at specific carrier solutions. The molecular weight of the natural MCDC was determined to be 208 kDa, which means it is a homotetramer, while that of the MCS was determined to be 47 kDa, which means it is a monomer.

• Journal of Microbiology and Biotechnology
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• v.31 no.10
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• pp.1393-1400
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• 2021

Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium Clostridium acetobutylicum has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the Clostridial host for ABE fermentation, C. acetobutylicum, (CaPTB) at a 2.9 Å resolution. The overall structure of the CaPTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of CaPTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of CaPTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of CaPTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.

• Proceedings of the Microbiological Society of Korea Conference
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• 2001.11a
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• pp.16-25
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• 2001

A genomic library of biphenyl-degrading strain Comamonas sp. SMN4 was constructed by using the cosmid vector pWE15 and introduced into Escherichia coli. Of 1,000 recombinant clones tested, two clones that expressed 2,3-dihydroxybiphenyl 1,2-dioxygenase activity were found (named pNB 1 and pNB2). From pNB1 clone, subclone pNA210, demonstrated 2,3-dihydroxybiphenyl 1,2-dioxygenase activity, is isolated. 2,3-Dihydroxybiphenyl 1,2-dioxygenase (23DBDO, BphC) is an extradiol-type dioxygenase that involved in third step of biphenyl degradation pathway. The nucleotide sequence of the Comamonas sp. SMN4 gene bphC, which encodes 23DBDO, was cloned into a plasmid pQE30. The His-tagged 23DBDO produced by a recombinant Escherichia coli, SG 13009 (pREP4)(pNPC), and purified with a Ni-nitrilotriacetic acid resin affinity column using the His-bind Qiagen system. The His-tagged 23DBDO construction was active. SDS-PAGE analysis of the purified active 23DBDO gave a single band of 32 kDa; this is in agreement with the size of the bphC coding region. The 23DBDO exhibited maximum activity at pH 9.0. The CD data for the pHs, showed that this enzyme had a typical a-helical folding structures at neutral pHs ranged from pH 4.5 to pH 9.0. This structure maintained up to pH 10.5. However, this high stable folding strucure was converted to unfolded structure in acidic region (pH 2.5) or in high pH (pH 12.0). The result of CD spectra observed with pH effects on 23DBDO activity, suggested that charge transition by pH change have affected change of conformational structure for 23DBDO catalytic reaction. The $K_m$ for 2,3-dihydroxybiphenyl, 3-metylcatechol, 4-methylcatechol and catechol was 11.7 $\mu$M, 24 $\mu$M, 50 mM and 625 $\mu$M.

• The Journal of Korean Medicine
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• v.27 no.2 s.66
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• pp.103-110
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• 2006

Objectives : This study was conducted to investigate the effects of ginseng saponins and commercial surfactants such as Triton X-100, sodium deoxycholate, and sodium dodecyl sulfate on the gastric enzyme-catalyzed hydrolysis. Methods : Saponins (a surface-active plant component) from fresh ginseng root were extracted to examine its effect on the gastric enzyme-catalyzed hydrolysis. Commercial surfactants such as Triton X-100, sodium deoxycholate, and sodium dodecyl sulfate were also employed in the hydrolysis system to compare their effects with that of the ginseng saponins. The effects of surfactants on the gastric enzyme-catalyzed hydrolysis were measured by using a spectrophotometer. A spectropolarimeter was used to examine the conformational change of enzymes and substrates by the addition of ginseng saponins into the system. Results : Both the tryptic and the peptic digestion of milk casein or eggalbumin were slightly improved with an increase in the amount of ginseng saponins in the system. Triton X-100 showed an effect similar to that of ginseng saponins, while sodium dodecyl sulfate and sodium deoxycholate diminished the hydrolysis. Circular dichroism spectra of enzymes and substrates was significantly changed by the addition of ginseng saponins into the system. Conclusions : These results show that ginseng saponins affect positively the gastric enzyme-catalyzed hydrolysis, and suggest that the digestion of substrates by gastric enzymes is affected by the change of enzyme conformation by ginseng saponins.

• BMB Reports
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• v.29 no.1
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• pp.32-37
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• 1996

The cysteine 43, potentially important in the activity of O-acetylserine sulfhydrylase (OASS) from Salmonella typhimurium, has been changed to serine. This mutant enzyme (C43S) has been studied in order to gain insight into the structural basis for the binding of inhibitor, substrate and product. UV-visible spectra of C43S exhibit the same spectral change in the presence of OAS as that observed with wild type enzyme, indicating C43S will form an ${\alpha}$-aminoacrylate Schiff base intermediate. At pH 6.5, however, the deacetylase activity of C43S is much higher than wild type enzyme indicating that cysteine 43 plays a role in stabilizing the ${\alpha}$-aminoacrylate intermediate. The fluoroscence spectrum of C43S exhibits a ratio of emission at 340 to 502 nm of 16.9, reflecting the lower fluorescence of PLP and indicating that the orientation of cofactor and tryptophan are different from that of the wild type enzyme. The emission spectrum of C43S in the presence of OAS gives two maxima at 340 and 535 nm. The 535 nm emission is attributed to the fluoroscence of the ${\alpha}$-aminoacrylate intermediate. The visible circular dichroic spectrum was similar to wild type enzyme, but the negative effect observed at 530~550 nm and the molar ellipicity values for the mutant are decreased by about 50% compared to wild type enzyme. The circular dichroic and fluoroscence studies suggest binding of the cofactor is less asymmetric in C43S than in the wild type enzyme.

• Applied Microscopy
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• v.35 no.4
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• pp.16-23
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• 2005

Peroxiredoxins (Prxs) are a superfamily of thiol-specific antioxidant proteins present in all organism and involved in the hydroperoxide detoxification of the cell. To determine the structural organization of yeast-Prx, electron microscopic analysis was performed. The average images of yeast-Prxs revealed three different structure, i.e. spherical-shaped structure, ring-shaped structure and irregularly-shaped small particles. In order to analyze the conformational change of yeast-Prx by reduction and oxidation, Prxs were subjected to DTT and $H_2O_2$. In presence of DTT, yeast-Prx showed a high tendency to form a decamer. However, they changed into dimeric or spherical structure in the oxidized state. Here we also show ionic interaction between dimeric subunits is primarily responsible for yeast-Prx oligomerization.

• BMB Reports
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• v.31 no.1
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• pp.25-30
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• 1998

Kinetic studies of L-Alanine dehydrogenase from Bacillus subtilis-catalyzed reactions in the presence of $Zn^{2+}$ were carried out. The substrate (L-alanine) saturation curve is hyperbolic in the absence of the metal ion but it becomes sigmoidal when $Zn^{2+}$ is added to the reaction mixture indicating the positive cooperative binding of the substrate in the presence of zinc ion. The cooperativity of substrate binding depends on the xinc ion concentration: the Hill coefficients ($n_H$) varied from 1.0 to 1.95 when the zinc ion concentration varied from 0 to $60\;{\mu}m$. The inhibition of AlaDH by $Zn^{2+}$ is reversible and noncompetitive with respect to $NAD^+$ ($K_i\;=\;5.28{\times}10^{-5}\;M$). $Zn^{2+}$ itself binds to AlaDH with positive cooperativity and the cooperativity is independent of substrate concentration. The Hill coefficients of substrate biding in the presence of $Zn^{2+}$ are not affected by the enzyme concentration indicating that $Zn^{2+}$ binding does not change the polymerization-depolymerization equilibria of the enzyme. Among other metal ions, $Zn^{2+}$ appears to be a specific reversible inhibitor inducing conformational change through the intersubunit interaction. These results indicate that $Zn^{2+}$ is an allosteric competitive inhibitor and substrate being a non-cooperative per se, excludes the $Zn^{2+}$ from its binding site and thus exhibits positive cooperativity. The allosteric mechanism of AlaDh from Bacillus subtilis is consistent with both MWC and Koshland's allosteric model.

• 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 the Korean Magnetic Resonance Society
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• v.20 no.2
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• pp.56-60
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• 2016

Adenylate kinase (AK) enzyme which acts as the catalyst of reversible high energy phosphorylation reaction between ATP and AMP which associate with energetic metabolism and nucleic acid synthesis and signal transmission. This enzyme has three distinct domains: Core, AMP binding domain (AMPbd) and Lid domain (LID). The primary role of AMPbd and LID is associated with conformational changes due to flexibility of two domains. Three dimensional structure of human AK1 has not been confirmed and various mutation experiments have been done to determine the active sites. In this study, AK1R138A which is changed arginine[138] of LID domain with alanine[138] was made and conducted with NMR experiments, backbone dynamics analysis and mo-lecular docking dynamic simulation to find the cause of structural change and substrate binding site. Synthetic human muscle type adenylate kinase 1 (hAK1) and its mutant (AK1R138A) were re-combinded with E. coli and expressed in M9 cell. Expressed proteins were purified and finally gained at 0.520 mM hAK1 and 0.252 mM AK1R138A. Multinuclear multidimensional NMR experiments including HNCA, HN(CO)CA, were conducted for amino acid sequence analysis and signal assignments of $^1H-^{15}N$ HSQC spectrum. Our chemical shift perturbation data is shown LID domain residues and around alanine[138] and per-turbation value(0.22ppm) of valine[179] is consid-ered as inter-communication effect with LID domain and the structural change between hAK1 and AK1R138A.

• Proceedings of the Korean Society for Emotion and Sensibility Conference
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• 2000.11a
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• pp.91-97
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• 2000

The conventional model did not take momentum conservation into consideration when the electron absorbs and emits the photons. II-ray provides momentum conservations on any directions of the entering photons, and also the electrons have radial momentum conservations and fully elastic bouncing between two atoms, in the new atom model. Conventional atom model must be criticized on the following four points. (1) Natural motions between positive and negative entities are not circular motions but linear going and returning ones, for examples sexual motion, tidal motion, day and night etc. Because the radius of hydrogen atom's electron orbit is the order of 10$^{-11}$ m and the radia of the nucleons in the nucleus are the order of 10$^{-l4}$m and then the converging n-gamma rays to the nucleus have so great circular momentum, the electron can not have a circular motion. We can say without doubt that any elementary mass particle can have only linear motion because of the n-rays' hindrances, near the nucleus. (2) Potential energy generation was neglected when electron changes its orbit from outer one to inner one. The h v is the kinetic energy of the photo-electron. The total energy difference between orbits comprises kinetic and potential energies. (3) The structure of the space must be taken into consideration because the properties of the electron do not change during the transition from outer orbit to inner one even though it produces photon. (4) Total energy conservation law applies to the energy flow between mind and matter because we daily experiences a interconnection between mind and body. An understanding of the mechanisms responsible for the control of normal proliferation and differentiation of the various cell types which make up the human body will undoubtedly allow a greater insight into the abnormal growth of cells, A large body of biochemical evidence was eventually used to generate a receptor model with an external ligand binding domain linked through a single trans-membrane domain to the cytoplasmic tyrosine kinase and autophosphory-lation domains. The ligand induced conformational change in the external domain generates either a push-pull or rotational signal which is transduced from the outside to the inside of cell.l.ell.