• Title/Summary/Keyword: cofactor binding

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Competitive Enzyme-Linked Immunosorbent Assay for Glucose-6-Phosphate Dehydrogenase

  • Kim, Moon-Hee
    • BMB Reports
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    • v.30 no.5
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    • pp.326-331
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    • 1997
  • To construct a competitive ELISA standard curve for the detection of glucose-6-phosphate debydrogenase (G6PD), we used highly purified native G6PD (nG6PD) as both immobilized and soluble antigens and anti-G6PD serum raised against nG6PD as antibody. The polystyrene cuvettes coated with nG6PD were challenged with a mixture of a limiting amount of anti-G6PD serum and various doses of nG6PD as competitors followed by incubation with alkaline phosphatase-anti-IgG conjugate. The competitive ELISA did not exhibit the typical sigmoidal dose-response curve characteristic of competition immunoassays under the optimal concentrations of antigen and antibody. The soluble nG6PD used as competitor failed to effectively inhibit the binding of antibodies to the immobilized nG6PD. The addition of NADP, a cofactor of G6PD enzyme, to coating buffer used for immobilizing nG6PD to the cuvettes and PBS-Tween-BSA buffer for diluting competitors did not improve the inhibition of antibody binding to immobilized nG6PD by soluble n/G6PD. The addition of BSA to coating buffer did not increase inhibition, either. Surprisingly, when partially active G6PD (paG6PD), obtained by repeated freeze-thawing, was used as competitor, the antibody binding to either immobilized nG6PD or immobilized paG6PD was inhibited 49-58%. We conclude that an effective competitive ELISA system with nG6PD enzyme and anti-G6PD serum for the detection of G6PD may not be established due to the poor inhibition of antibody binding to immobilized nG6PD by soluble nG6PD under the present assay conditions and that the inhibition may be improved by using an inactivated enzyme as competitor regardless of the type of immobilized antigen used. These results imply that the immobilized nG6PD may undergo denaturation upon binding to the polystyrene cuvettes and that our anti-G6PD serum may recognize denatured enzyme better than active enzyme.

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Ginsenoside F2 Restrains Hepatic Steatosis and Inflammation by Altering the Binding Affinity of Liver X Receptor Coregulators

  • Kyurae Kim;Myung-Ho Kim;Ji In Kang;Jong-In Baek;Byeong-Min Jeon;Ho Min Kim;Sun-Chang Kim;Won-Il Jeong
    • Journal of Ginseng Research
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    • v.48 no.1
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    • pp.89-97
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    • 2024
  • Background: Ginsenoside F2 (GF2), the protopanaxadiol-type constituent in Panax ginseng, has been reported to attenuate metabolic dysfunction-associated steatotic liver disease (MASLD). However, the mechanism of action is not fully understood. Here, this study investigates the molecular mechanism by which GF2 regulates MASLD progression through liver X receptor (LXR). Methods: To demonstrate the effect of GF2 on LXR activity, computational modeling of protein-ligand binding, Time-resolved fluorescence resonance energy transfer (TR-FRET) assay for LXR cofactor recruitment, and luciferase reporter assay were performed. LXR agonist T0901317 was used for LXR activation in hepatocytes and macrophages. MASLD was induced by high-fat diet (HFD) feeding with or without GF2 administration in WT and LXRα-/- mice. Results: Computational modeling showed that GF2 had a high affinity with LXRα. LXRE-luciferase reporter assay with amino acid substitution at the predicted ligand binding site revealed that the S264 residue of LXRα was the crucial interaction site of GF2. TR-FRET assay demonstrated that GF2 suppressed LXRα activity by favoring the binding of corepressors to LXRα while inhibiting the accessibility of coactivators. In vitro, GF2 treatments reduced T0901317-induced fat accumulation and pro-inflammatory cytokine expression in hepatocytes and macrophages, respectively. Consistently, GF2 administration ameliorated hepatic steatohepatitis and improved glucose or insulin tolerance in WT but not in LXRα-/- mice. Conclusion: GF2 alters the binding affinities of LXRα coregulators, thereby interrupting hepatic steatosis and inflammation in macrophages. Therefore, we propose that GF2 might be a potential therapeutic agent for the intervention in patients with MASLD.

Interaction of Norfloxacin with Super-Coiled DNA

  • Hwangbo, Hyun-Jung;Lee, Young-Ae;Park, Jung-Hag;Lee, Yong-Rok;Kim, Jong-Moon;Yi, Seh-Yoon;Kim, Seog K.
    • Bulletin of the Korean Chemical Society
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    • v.24 no.5
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    • pp.579-582
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    • 2003
  • Norfloxacin, that inhibits the action of topoisomerase Ⅱ, binds to wide variety of DNA. The binding mode of this drug to double- and super-coiled DNA (ds- and scDNA) is compared in this study by various spectroscopic methods, including absorption, fluorescence, and circular dichroism(CD) spectroscopy. Hypochromism in the absorption band, negative and positive induced CD bands (respectively in 240-260 nm and 270-300 nm region) are apparent for the norfloxacin that bound to both the dsDNA and scDNA. A decrease in fluorescence is also noticed in the presence of both DNAs. Since the spectroscopic characteristics are the same for both complexes, it is imperative that the binding mode of the norfloxacin is similar in ds- and scDNA. In the presence of $Mg^{2+}$, which is a cofactor in the topoisomerase Ⅱ action, the fluorescence intensity of the scDNA-norfloxacin complex increased and the resulting fluorescence intensity and shape was identical to that in the absence of scDNA. Therefore, the addition of an excess amount of $Mg^{2+}$ may result in the extrusion of norfloxacin from scDNA.

Regulatory Mechanism of L-Alanine Dehydrogenase from Bacillus subtilis

  • Kim, Su Ja;Kim, Yu Jin;Seo, Mi Ran;Jeon, Bong Suk
    • Bulletin of the Korean Chemical Society
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    • v.21 no.12
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    • pp.1217-1221
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    • 2000
  • L-alanine dehydrogenase from Bacillus subtilis exhibits allosteric kinetic properties in the presence of $ZN^{2+}$. $ZN^{2+}$ induces the binding of substrate (L-alanine) to be cooperative at pH 8.0. The effect of pH variation between pH 7.0 and pH 10.0 on the inhibition by $ZN^{2+}$ correlates with the pH effect on the $K_m$ values for L-alanine within these pH range indicating that $ZN^{2+}$ and substrate compete for the same site. No such cooperativity is induced by $ZN^{2+}$ when the reaction is carried out at pH 10. At this higher pH, $ZN^{2+}$ binds with the enzyme with lower affinity and noncompetitive with respect to L-alanine. Inhibition of L-alanine dehydrogenase by $ZN^{2+}$ depends on the ionic strength. Increase in KCI concentration reduced the inhibition, but allosteric property in $ZN^{2+}$ binding is conserved. A model for the regulatory mechanism of L-alanine dehydrogenase as a noncooperative substrate-cooperative cofactor allosteric enzyme, which is compatible in both concerted and the sequential allosteric mechanism, is proposed.

Inactivation of Brain GABA transaminase by p$^1$, p$^2$-Bis(5′-pyridoxal) diphosphate

  • Jang, S.H.;Lee, B.R.;J.W. Hong;Park, K.W.;Yoo, B.K.;Cho, S.W.;Park, S.Y.
    • Proceedings of the Korean Society of Applied Pharmacology
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    • 1995.04a
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    • pp.74-74
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    • 1995
  • GABA transaminase is inactivated by preincubation with p$^1$, p$^2$-bis(5'-pyridoxal) diphosphate at pH 7.0. The inactivation under pseudo-first order conditions proceeds at a slow rate (K$\_$obs/=0.035 min$\^$-1/). The degree of labeling of the enzyme by p$^1$, p$^2$-bis(5'-pyridoxal) diphosphate was determined by absorption spectroscopy, The blocking of 2 lysyl residues/dimer is needed for inactivation of the transaminase. The time course of the reaction is significantly affected by the substrate ${\alpha}$-ketoglutarate, which afforded complete protection against the loss of the catalytic activity. Whereas cofator pyridoxal phosphate failed to prevent the inactivation of the enzyme. Therefore, it is postulated that binding of ${\alpha}$-ketoglutarate tn lysyl residues is the major factor contributing to stabilization of the catalytic site and bifuctional reagent p$^1$, p$^2$bis(5'-pyridoxal) diphosphate blocks lysyl residues other than those involved in the binding of the cofactor.

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Kinetics and Mechanism of Mutant O-acetylserine Sulfhydrylase-A (C43S) from Salmonella typhimurium LT-2

  • Yoon, Moon-Young
    • BMB Reports
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    • v.29 no.3
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    • pp.210-214
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    • 1996
  • The pH dependence of the kinetic parameters of mutant O-acetylserine sulfhydrylase (OASS) from Salmonella typhimurium LT-2 has been determined in order to obtain information on the chemical mechanism. The initial velocity pattern obtained by varying the concentrations of OAS at several fixed concentrations of TNB, shows an intersection on the left of the ordinate at pH 7.0, indicating that the kinetic mechanism is a sequential mechanism in which substrate inhibition by OAS is observed while the wild type enzyme showed a ping pong mechanism. The values of $V/E_t$, $V/K_{OAS}E_{t}$ and $V/K_{TNB}E_{t}$ decreased by about 68%, 14% and 16% as compared with the wild type enzyme. The $V/K_{OAS}E_{t}$ is a pK of 6.5 on the acid side of the pH profile, and the $V/K_{TNB}$ is pH independent. As compared with the wild type enzyme, the pKs in the V/K profiles are shifted, reflecting that binding of the cofactor in free E:OAS is less asymmetric.

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Site-Directed Mutagenesis of Ile91 of Restriction Endonuclease EcoRV: Dramatic Consequences on the Activity and the Properties of the Enzyme

  • Moon, Byung-Jo;Vipond, I. Barry;Halford, Stephen E.
    • BMB Reports
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    • v.29 no.1
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    • pp.17-21
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    • 1996
  • Ile91 of restriction endonuclease EcoRV, which has not been known to take part directly in catalytic activity, was substituted with Leu by site-directed mutagenesis. The Ile91Leu mutant shows over 1000-fold less activity than the wild type EcoRV under standard reaction condition. The metal ion dependency of the reaction was altered. In contrast to the wild type EcoRV, the mutant prefers $Mn^{2+}$ to $Mn^{2+}$ as the cofactor. In $Mn^{2+}$ buffer the mutant is as active as the wild type enzyme in $Mn^{2+}$ buffer. Like the wild type enzyme, the mutant shows an unspecific binding of DNA in gel shift experiments. In contrast to the wild type enzyme, the mutant did not cleave at noncognate sites of DNA under star condition.

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Biological roles and an evolutionary sketch of the GRF-GIF transcriptional complex in plants

  • Kim, Jeong Hoe
    • BMB Reports
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    • v.52 no.4
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    • pp.227-238
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    • 2019
  • GROWTH-REGULATING FACTORs (GRFs) are sequence-specific DNA-binding transcription factors that regulate various aspects of plant growth and development. GRF proteins interact with a transcription cofactor, GRF-INTERACTING FACTOR (GIF), to form a functional transcriptional complex. For its activities, the GRF-GIF duo requires the SWITCH2/SUCROSE NONFERMENTING2 chromatin remodeling complex. One of the most conspicuous roles of the duo is conferring the meristematic potential on the proliferative and formative cells during organogenesis. GRF expression is post-transcriptionally down-regulated by microRNA396 (miR396), thus constructing the GRF-GIF-miR396 module and fine-tuning the duo's action. Since the last comprehensive review articles were published over three years ago, many studies have added further insight into its action and elucidated new biological roles. The current review highlights recent advances in our understanding of how the GRF-GIF-miR396 module regulates plant growth and development. In addition, I revise the previous view on the evolutionary origin of the GRF gene family.

Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase

  • Tran, Huyen-Thi;Lee, Seon-Hwa;Ho, Thien-Hoang;Hong, Seung-Hye;Huynh, Kim-Hung;Ahn, Yeh-Jin;Oh, Deok-Kun;Kang, Lin-Woo
    • BMB Reports
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    • v.49 no.12
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    • pp.681-686
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    • 2016
  • Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between $1.8{\AA}$ and $2.0{\AA}$. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for $Zn^{2+}$ ion. Citrate and TRIS bound EcFBA structures showed $Zn^{2+}$ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor $Zn^{2+}$ within EcFBA without losing it.

Biochemical characterization of Alanine racemase- a spore protein produced by Bacillus anthracis

  • Kanodia, Shivani;Agarwal, Shivangi;Singh, Priyanka;Agarwal, Shivani;Singh, Preeti;Bhatnagar, Rakesh
    • BMB Reports
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    • v.42 no.1
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    • pp.47-52
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    • 2009
  • Alanine racemase catalyzes the interconversion of L-alanine and D-alanine and plays a crucial role in spore germination and cell wall biosynthesis. In this study, alanine racemase produced by Bacillus anthracis was expressed and purified as a monomer in Escherichia coli and the importance of lysine 41 in the cofactor binding octapeptide and tyrosine 270 in catalysis was evaluated. The native enzyme exhibited an apparent $K_m$ of 3 mM for L-alanine, and a $V_{max}$ of $295\;{\mu}moles/min/mg$, with the optimum activity occurring at $37^{\circ}C$ and a pH of 8-9. The activity observed in the absence of exogenous pyridoxal 5'-phosphate suggested that the cofactor is bound to the enzyme. Additionally, the UV-visible absorption spectra indicated that the activity was pH independece, of VV-visible absorption spectra suggests that the bound PLP exists as a protonated Schiff's base. Furthermore, the loss of activity observed in the apoenzyme suggested that bound PLP is required for catalysis. Finally, the enzyme followed non-competitive and mixed inhibition kinetics for hydroxylamine and propionate with a $K_i$of $160\;{\mu}M$ and 30 mM, respectively.