• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.305-307
• /
• 2002

Spectroscopic titration of D 193N and D 193E mutants of pharaonis phoborhodopsin (ppR) were performed to evaluate the pK$_{a}$ of the Schiff base Asp 193 corresponds to Glu204 of bacteriorhodopsin (bR). The pK$_{a}$ of the Schiff base (SBH$^{+}$) of D193N was 10.1~10.0 (at XH$^{+}$) and 11.4~11.6 (at X) depending on the protonation state of a certain residue (designated by X) and independent on CI$^{[-10]}$ , while those of the wild-type and D193E were> 12. pK$_{a}$ of XH$^{+}$ were; 11.8~11.2 at the state of SB, 10.5 at SBH$^{+}$ state in the presence of CI$^{[-10]}$ , and 9.6 at SBH$^{+}$ without CI$^{[-10]}$ These imply the presence of a long-range interaction in the extracellular channel.r channel.

• Proceedings of the Korean Biophysical Society Conference
• /
• 1998.06a
• /
• pp.21-21
• /
• 1998

Since the repair efficiency of non-Watson-Crick base pairs in DNA is affected by the mismatched base-pairs and their neighbor sequences, the structural studies are necessary for the elucidation of the repair efficiency. NMR and molecular modeling studies on the DNA duplexes including AA mismatches were performed.(omitted)

• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.302-304
• /
• 2002

pharaonis phoborhodopsin (ppR), a photophobic sensor of haloalkaliphilic bacteria, Natronobacterium phar-aonis, has retinal as a chromophore covalently bound to Lys in G-helix via a protonated Schiff base (PSB), as is the same as bacteriorhodopsin (bR). For ppR, the corresponding counter-ion is Asp residue (Asp75) located in C-helix. Here we investigated the influence of the protonated state of this counter-ion and its location on the chromophore configuration. Under alkaline condition, the chromophore configuration of D75E mutant was analyzed by HPLC. D75E had a much larger content of 13-cis isomer: the ratio of 13-cis to all-trans was 6:4 while the wild-type had this ratio of 1 :9. On the other hand, under acidic condition where Glu was associated, D75E had no 13-cis retinal isomer. Mutants whose Asp75 was replaced by neutral amino acids (D75N and D75Q) did not contain 13-cis retinal. Furthermore, retinal isomer compositions and the change in the visible ab- sorption spectra (indicating the dissociation state of Glu75) were measured under varying pH, and these were almost the same dependencies. These results indicate that an important factor determining the 13-cis isomer content is the presence of negative charge of the counter-ion against PSB, but not the size of this residue. Com- parison between the wild-type and D75E in alkaline solutions indicates the influence of the location of the counter-ion.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.9
• /
• pp.1973-1977
• /
• 2009

In the present study, at first, 2,4-Dihydroxy Salophen (2,4-DHS), has been synthesized by combination of 1, 2-diaminobenzene and 2,4-dihydroxybenzaldehyde in a solvent system. This ligand containing meta-quinone functional groups were characterized using UV-Vis and IR spectroscopies. Subsequently, the interaction between native calf thymus deoxyribonucleic acid (ct-DNA) and 2,4-DHS, was investigated in 10 mM Tris/HCl buffer solution, pH 7.2, using UV-visible absorption and fluorescence spectroscopies, thermal denaturation technique and viscosity measurements. From spectrophotometric titration experiments, the binding constant of 2,4-DHS with ct-DNA was found to be (1.1 ${\pm}\;0.2)\;{\times}\;10^4\;M^{-1}.$ The fluorescence study represents the quenching effect of 2,4-DHS on bound ethidium bromide to DNA. The quenching process obeys linear Stern-Volmer equation in extended range of 2,4-DHS concentration. Thermal denaturation experiments represent the increasing of melting temperature of DNA (about 3.5 ${^{\circ}C}$) due to binding of 2,4-DHS. These results are consistent with a binding mode dominated by interactions with the groove of ct-DNA.

• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.311-313
• /
• 2002

X-ray structures of pharaonis phoborhodopsin (ppR) show the different direction of the side chain of Arg72 from that of the corresponding residue (Arg82) of bacteriorhodopsin, BR. For BR, this residue is considered to play an important role in the proton pumping. In order to investigate the role of Arg72 in ppR, we constructed Arg72 mutants of R72A, R72K and R72Q, and measured the photocycle and proton pumping activities. The pH-titration curves on the absorption maximum of the mutants were shifted to alkaline in comparison of that of the wild-type. This may imply the increase of pKa of D75, suggesting the presence of the (probably electric) interaction between D75 and Arg72. Rate constants of the M-decay were 3-7 times faster than that of the wild-type, and the time for the completion of the photocycling was also reduced. Using Sn0$_2$ electrode, the rate of transmembrane proton transport was measured upon illumination. The photo-induced proton pumping activities were estimated after the corrections that are the percentages of the associated form of D75 (which has no pumping activity) and the photocycling rates. R72A and R72Q showed the reduced activity while R72K did not reduce the activity.

• Proceedings of the Korean Biophysical Society Conference
• /
• 2001.06a
• /
• pp.27-27
• /
• 2001

In exocrine acinar cells, $Ca^{2＋}$ -activated Cl$^{[-10]}$ channels in the apical membrane are essential for fluid secretion, but it is unclear whether such channels are important for Cl$^{[-10]}$ uptake at the base. Whole cell current recording, combined with local uncaging of caged $Ca^{2＋}$, was used to reveal the Cl$^{[-10]}$ channel distribution in mouse pancreatic acinar cells, where ~90％ of the current activated by $Ca^{2＋}$ in response toacetylcholine was carried by Cl$^{[-10]}$ .(omitted)

• Proceedings of the Korean Biophysical Society Conference
• /
• 1999.06a
• /
• pp.36-36
• /
• 1999

Bacterial Δ-3-ketosteroid isomerase (KSI) catalyzes the conversion of Δ-to Δ-3-ketosteroids via enolate formation, which is also found in the synthesis of all steroid hormones in mammals. In Pseudomonas testosteroni, KSI Asp38 (pKa ~ 4.7) was identified as the general base which abstracts the steroid C4b-H (pKa ~ 12.7) to form the dienolate intermediate.(omitted)

• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.106-109
• /
• 2002

Archaeal rhodopsins possess retinal molecule as their chromophores, and their light-energy and light-signal conversions are triggered by all-trans to 13-cis isomerization of the retinal chromophore. Relaxation through structural changes of protein then leads to functional processes, proton pump in bacteriorhodopsin (bR) and transducer activation in phoborhodopsin (pR). It is known that sensory rhodopsins can pump protons in the absence of their transducers. Thus, there should be common and specific features in their protein structural changes for function. In this paper, our r ecent studies on pR from Natronobacterium pharaonis (ppR) by means of low-temperature Fourier-transform infrared (FTIR) spectroscopy are compared with those of bR. In particular, protein structural changes upon retinal photoisomerization are studied. Comparative investigation of ppR and bR revealed the similar structures of the polyene chain of the chromophore and water-containing hydrogen-bonding network, whereas the structural changes upon photoisomerization were more extended in ppR than in bR. Extended protein structural changes were clearly shown by the assignment of the C=O stretch of Asnl05. FTIR studies of a ppR mutant with the same retinal binding site as in bR revealed that the Schiff base region is important to determine their colors.

• Journal of Environmental Science International
• /
• v.26 no.9
• /
• pp.1087-1099
• /
• 2017

Emergy methodology was used to analyze the biophysical basis of Korean agriculture and assess its sustainablility. Total yearly emergy input into Korean agriculture was $7.72{\times}10^{22}sej/yr$ in 2013. Purchased inputs were the dominant emergy source, accounting for 90.1% ($6.95{\times}10^{22}sej/yr$) of the annual input. This clearly indicates that the Korean agriculture is a modern, industrialized system that depends mostly on market goods and services derived from nonrenewable resources. The monetary equivalent of the total emergy input was 18.9 trillion \/yr, 1.5 times greater than the total production cost from farm expense surveys. Emergy return on investment of Korean agriculture was low, with an emergy yield ratio of 1.11. Korean agriculture appears to exert pressure on the environment as revealed by the high environmental loading ratio of 9.30. With very low emergy input from renewable sources (9.7%) and high environmental pressure, Korean agriculture is not sustainable, with an emergy sustainability index of 0.12. This study suggests that higher use efficiency of and lower dependence on nonrenewable purchased inputs need to be prioritized in an effort to enhance the sustainability of Korean agriculture.

• BMB Reports
• /
• v.42 no.6
• /
• pp.373-379
• /
• 2009

5-Hydroxyuridine (5-OHU) is a major lesion of uridine and cytosine produced in RNA by various chemical oxidants. To elucidate its biochemical and biophysical effects on RNA replication, the site-specifically modified oligoribonucleotides containing 5-OHU were synthesized with C5-hydroxy-5'-ODMTr-2'-TBDMS-uridine phosphoramidite using automated solid phase synthesis. The base-pairing properties of nucleotides opposite 5-OHU in 24 mer oligoribonulcleotides with dNTP were studied using three reverse transcriptases (Super-$Script^{TM}II$-, AMV-, MMLV-RT) in cDNA synthesis. Adenine as well as guanine was incorporated preferentially by all reverse transcriptases. In the UV-melting temperature experiment, the results from the relative stabilities of the base pairs were A : 5-OHU > G : 5-OHU > T : 5-OHU $\approx$ C : 5-OHU. Circular Dichroism (CD) studies showed that DNA-RNA containing 5- OHU heteroduplexes exhibit a similar conformation between the A-type RNA and B-type DNA. These results suggest that 5- OHU from oxidative damage was mainly influenced by adenine mismatch.