• Journal of Life Science
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• v.15 no.6 s.73
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• pp.935-940
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• 2005

Fluorescence change of coumarin labeled phosphate binding protein (PBP-MDCC) was monitored to measure the amount of released inorganic phosphate ($P_{i}$) during nucleoside triphosphate (NTP) hydrolysis reaction. After purification of PBP-MDCC, fluorescence emission spectra showed that fluorescence responded linearly to $P_{i}$ up to about 0.7 molar ratio of $P_{i}$ to protein. The correlation of fluorescence signal and $P_{i}$ standard was measured to obtain [$P_{i}$] - fluorescence intensity standard curve on the stopped-flow instrument. When T7 bacteriophage helicase, double-stranded DNA unwinding enzyme using dTTP hydrolysis as an energy source, reacted with dTTP, the change of fluorescence was able to be converted to the amount of released $P_{i}$ by the $P_{i}$ standard curve. $P_{i}$ release results showed that single-stranded Ml3 DNA stimulated dTTP hydrolysis reaction several folds by T7 helicase. Instead of end point assay in NTP hydrolysis reaction, real time $P_{i}$-release assay by PBP-MDCC was proven to be very easy and convenient to measure released $P_{i}$.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.1
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• pp.23-34
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• 2004

Escherichia coli transcription termination factor Rho catalyzes the unwinding of RNA/DNA duplex in reactions that are coupled to ATP binding and hydrolysis. Fluorescence stopped-flow methods using ATP and the fluorescent 2'(3')-O-( N-methylanthraniloyl) derivatives (mant-derivatives) of ATP and ADP were used to probe the kinetics of nucleotide binding to and dissociation from the Rho-RNA complex. Presteady state nucleotide binding kinetics provides evidence for the presence of negative cooperativity in nucleotide binding among the multiple nucleotide binding sites on Rho hexamer. The binding of the first nucleotide to the Rho-RNA complex occurs at a bimolecular rate of 3.6${\times}$10$\^$6/ M$\^$-1/ sec$\^$-1/ whereas the second nucleotide binds at a slower rate of 4.7${\times}$10$\^$5/ M$\^$-1/ sec$\^$-1/ at 18$^{\circ}C$, RNA complexed with Rho affects the kinetics of nucleotide interaction with the active sites through conformational changes to the Rho hexamer, allowing the incoming nucleotide to be more accessible to the sites. Adenine nucleotide binding and dissociation is more favorable when RNA is bound to Rho, whereas ATP binding and dissociation step in the absence of RNA occurs significantly slower, at a rate ∼70- and ∼40-fold slower than those observed with the Rho-RNA complex, respectively.

• BMB Reports
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• v.40 no.4
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• pp.453-458
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• 2007

Bacterial luciferase is a heterodimeric enzyme, which catalyzes the light emission reaction, utilizing reduced FMN (FMNH2), a long chain aliphatic aldehyde and $O_2$, to produce green-blue light. This enzyme can be readily classed as slow or fast decay based on their rate of luminescence decay in a single turnover. Mutation of Glu175 in $\alpha$ subunit to Gly converted slow decay Xenorhabdus Luminescence luciferase to fast decay one. The following studies revealed that changing the luciferase flexibility and lake of Glu-flavin interactions are responsible for the unusual kinetic properties of mutant enzyme. Optical and thermodynamics studies have caused a decrease in free energy and anisotropy of mutant enzyme. Moreover, the role of Glu175 in transition state of folding pathway by use of stopped-flow fluorescence technique has been studied which suggesting that Glu175 is not involved in transition state of folding and appears as surface residue of the nucleus or as a member of one of a few alternative folding nuclei. These results suggest that mutation of Glu175 to Gly extended the structure of Xenorhabdus Luminescence luciferase, locally.

• Bulletin of the Korean Chemical Society
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• v.31 no.10
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• pp.2877-2883
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• 2010

The folding kinetics of $WT^*$ ubiquitin variant with valine to alanine mutation at sequence position 26 (HubWA) was studied by stopped-flow fluorescence spectroscopy. While unfolding kinetics showed a single exponential phase, refolding reaction showed three exponential phases. The semi-logarithmic plot of urea concentration vs. rate constant for the first phase showed v-shape pattern while the second phase showed v-shape with roll-over effect at low urea concentration. The rate constant and the amplitude of the third phase were constant throughout the urea concentrations, suggesting that this phase represents parallel process due to the configurational isomerization. Interestingly, the first and second phases appeared to be coupled since the amplitude of the second phase increased at the expense of the amplitude of the first phase in increasing urea concentrations. This observation together with the roll-over effect in the second folding phase indicates the presence of intermediate state during the folding reaction of HubWA. Quantitative analysis of Hub-WA folding kinetics indicated that this intermediate state is on the folding pathway. Folding kinetics measurement of a mutant HubWA with hydrophobic core residue mutation, Val to Ala at residue position 17, suggested that the intermediate state has significant amount of native interactions, supporting the interpretation that the intermediate is on the folding pathway. It is considered that HubWA is a useful model protein to study the contribution of residues to protein folding process using folding kinetics measurements in conjunction with protein engineering.

• Journal of the Korean Society of Food Science and Nutrition
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• v.26 no.4
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• pp.743-750
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• 1997

Direct measurement of the kinetics of free fatty acid transfer between phospholipid model membrane is technically limited by the rapid nature of the transfer process. Separation of membrane-bound fatty acid by centrifugation has shown that although the equilibrium distribution of free fatty acid is determined by this method, fatty acid transfer occurs too rapidly for accurate kinetic measurements. Recently fluorescence resonance energy transfer(FRET) assay has been developed to examine transfer of fatty acids between membranes. Donor membranes which has fluorescent fatty acid, anthroyloxy fatty acid(AOFA), is mixed with acceptor membranes which has non-interchangeable fluorescent quencher, nitrobenzo-xadiazol(NBD), using stopped flow apparatus. As the fluorescent fatty acids transfer from donor membrane to acceptor membrane, fluorescence intensity would be decreased and the rate and degree of fatty acid transfer can be analyzed. Fatty acid transfer between micelles is more complicated because of bile salt. Therefore in experiments with micelles, fluorescence self quenching assay is used. At high concentrations, a fluorophore tends to quench its own fluorescence causing a reduction in fluorescence intensity. Donor micelles contained self quenching concentrations of fluorophore and acceptor micelles had no fluorophore. Upon mixing of donor and acceptor micelles, the rate of transfer of the fluorophore from the donor to the acceptor was measured by monitoring the release in self quenching when its concentration in donor decreased over time.

• The Korean Journal of Physiology
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• v.28 no.2
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• pp.203-214
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• 1994

Using the methods of stopped-flow and epifluorescence microscopy with entrapped fluorophore, membrane permeability of $NH_3$ and weak acids in liposomes, renal brush border (BBMV) and basolateral membrane vesicles (BLMV), and primary culture cells from renal proximal tubule was measured. Permeability coefficient (cm/sec) of $NH_3$ was $(2.9{\times}10^{-2}$ in phosphatidylcholine liposome $25^{\circ}C)$, $5.9{\times}10^{-2}$ in renal proximal tubule cell $(37^{\circ}C)$, $4.0{\times}10^{-2}\;and\;2.4{\times}10^{-2}$ in BBMV and BLMV $(25^{\circ}C)$, respectively. Formic acid has the highest permeability coefficient among the weak acids tested, which was $4.9{\times}10^{-3}$ in liposome, $5.0{\times}10^{-3}$ in renal proximal tubule cell, $9.1{\times}10^{-3}$ in BBMV and $3.8{\times}10^{-3}$ in BLMV. There was a linear relationship between external concentration of nonionized formic acid and initial rate of flux of formic acid in liposome, and the slope coincided with the value of permeability coefficient of formic acid measured in pH 7.0. These results show that techniques of stopped-flow and epifluorescence microscopy with entrapped fluorophore provide the precise method of measurement of very rapid transport of nonelectrolytes through membranes with the advantages of instantaneous mixing effect, good resolution time and easy manipulation.

• Bulletin of the Korean Chemical Society
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• v.30 no.7
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• pp.1567-1572
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• 2009

Conformational change of ubiquitin variant with valine to alanine mutation at sequence position 26 was studied by varying solvent pH. Fluorescence emission spectra indicated that this variant ubiquitin has some residual structures in acidic and basic solution as compared to denaturant-induced unfolded state. Far-UV circular dichroic spectra indicated that the base-denatured state had more secondary structure than the acid-denatured state. Near-UV circular dichroic spectra indicated that the aromatic side-chains were in the relatively more rigid environment in the base-denatured state than those in the acid-denatured state. Although it appears that the more tertiary structure present in the base-denatured state, refolding reactions measured by stopped-flow fluorescence device suggest that both the acid- and base-denatured states occur before the major folding transition state. The acid- and base-denatured states are considered to reflect the early event of protein folding process.

• Journal of the Korean Chemical Society
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• v.38 no.11
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• pp.792-799
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• 1994

The spectral changes of 3,3'-diethyl oxacarbocyanine(DOC) in the aqueous solution and in the presence of polyacrylic acid(PAA) were studied by means of absorption and fluorescence spectroscopy. The spectral change of DOC in the aqueous solution with concentration changes is attributed to the formation of dimer. In the presence of PAA, the characteristic changes of metachromatic band with changes of P/D (the ratio between available binding site and the dye concentration) are found and the discussions are made in terms of stacking theory. A kinetic study of the interaction between DOC and PAA was also investigated by the absorption and fluorescence stopped-flow spectroscopy. The observed relaxation effect in PAA-DOC system can be described quantitatively by assuming two relaxation processes occur.

• Journal of the Korean Chemical Society
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• v.39 no.8
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• pp.604-610
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• 1995

The interaction between 3,3'-dipropyl oxacarbocyanine and poly(styrenesulfonate) has been studied by means of absorption and fluorescence spectroscopic methods. The results was interpreted by stacking model. The kinetic studies of the interaction between 3,3'-dipropyl oxacarbocyanine and poly(styrenesulfonate) were carried out by the absorption and fluorescence spectroscopic stopped-flow methods. The observed relaxation effect in DPC-PSS system was described quantitatively by assuming two relaxation processes. The dependence of rate of reaction on the salt concentration of the solution was also studied. The results are consistent with the two-step mechanism.

• Journal of the Korean Chemical Society
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• v.63 no.6
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• pp.427-434
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• 2019

The role of hydrophobic residues on protein folding reaction was studied by folding kinetics measurements in conjunction with protein engineering. The HubWA, which was derived from human ubiquitin by mutating the residues at 45 (Phe to Trp) and 26 (Val to Ala), was used as a mutational background. Fourteen hydrophobic residues were mutated to alanine. Among fourteen variants generated, only four variant proteins (V5A, I13A, V17A, and I36A) were suitable for folding study. The folding kinetics of these variants was measured by stopped-flow fluorescence spectroscopy. The folding kinetics of HubWA and V17A was observed to follow a three-state on-pathway mechanism. On the other hand, folding kinetics of V5A, I13A, and I36A was observed to follow a two-state mechanism. Based on these observations, transition of protein folding reaction from collision-diffusion mechanism to nucleation-condensation mechanism was discussed.