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S Kaminaka

Publications and source records attributed to S Kaminaka.

7 recordsLinked to original sources
PubMed1999

Studies of bovine enterovirus structure by ultraviolet resonance Raman spectroscopy.

The structural comparison of bovine enterovirus MZ468 strain before and after the heat treatment was studied by ultraviolet resonance Raman (UVRR) spectra excited at both 235 and 251 nm. The difference between full, heated full and purified empty particles, which were expected as an in vitro model of uncoating, were demonstrated. At 235 nm excitation, the Raman bands of the capsid protein dominated in all the UVRR spectra. The UVRR spectra of the empty particles exhibited non-homogenious broadening for tryptophan W3 band and W7 Fermi doublet bands, which were characteristics of hydrophobic environment, when compared with those of the full particles. The results indicates that some Trp indole rings of the full particles were packaged inside the viral capsids and not strained by virion assembly. On the other hand, the Raman bands assigned to guanine residues of the single stranded-RNA genome were enhanced strongly in the 251-nm excited UVRR spectrum. The spectral differences between the packaged (full particles) and the unpackaged virions (heated full particles) indicates that some guanine residues had strong hydrogen bonds in the full particles.

Animals↗
PubMed1997

Ultraviolet resonance Raman examination of the light-induced protein structural changes in rhodopsin activation.

Ultraviolet resonance Raman (UVRR) spectra of rhodopsin and its metarhodopsin I and metarhodopsin II photointermediates have been obtained to examine the molecular mechanism of G-protein-coupled receptor activation. Spectra were acquired using a single-pass capillary flow technique in combination with a Littrow prism UV prefilter detection system. The UVRR difference spectra between rhodopsin and mearhodopsin I exhibit small differences assignalbe to tyrosine residues and no differences due to tryptophan. The UVRR difference spectra between rhodopsin and metarhodopsin II exhibit significant differences for vibrations of both tryptophan and tyrosine residues. Most importantly, there is and intensity decrease of the totally symmetric tryptophan modes at 759, 1008, and 1545 cm-1, an intensity decrease of the tryptophan W7 band at 1357 cm-1, and a frequency shift of the tryptophan W17 ban from 885 to 892 cm-1. These difference features are assigned to one or more tryptophan residues that reside in a hydrophobic, weakly hydrogen-bonding environment in rhodopsin and that are transferred to a less hydrophobic, non-hydrogen-bonding environment during rhodopsin activation. The available evidence suggests that Trp265 makes a dominant contribution to the tryptophan features in this difference spectrum. These results are interpreted with a model for rhodopsin activation in which retinal isomerization alters the interaction of Trp265 with the ionone ring of the retinal chromophore.

Animals↗
PubMed1997

A 55-kDa endonuclease of mammalian mitochondria: comparison of its subcellular localization and endonucleolytic properties with those of endonuclease G.

A novel endonuclease of 55-kDa was found in rat liver mitochondria by a zymographic assay, in addition to the 29 kDa enzyme that is well-known as endonuclease G (Endo G). Subcellular localization of these enzymes in rat liver cells was examined by biochemical fractionation. Endo G was located in both nuclei and mitochondria as has been previously reported, while the 55-kDa enzyme was only detected in the mitochondrial fraction. The levels of the endonucleases in the mitochondria varied greatly among the rat organs, and the activity in the heart was about 30 times higher than that in the liver. The 55-kDa enzyme and Endo G were extracted from bovine heart mitochondria with 0.4 M NaCl. During purification the 55-kDa enzyme and Endo G were copurified because of their similar chromatographic behavior, so they were separated by gel filtration or electrophoresis in the presence of SDS and the proteins were then renatured. The nucleolytic properties of the 55-kDa enzyme resembled those of Endo G and other known mitochondrial nucleases. The enzyme degraded single-stranded DNA more rapidly than duplex DNA at a weak alkaline pH1 requiring Mg2+ or Mn2+ but not Ca2+ or Zn2+. Nicks generated by the enzyme had 5'-P and 3'-OH ends. The 55-kDa enzyme, like Endo G, displayed an unusually strong preference to nick within a (dG)n.(dC)n tract.

Animals↗
PubMed1995

Ultraviolet resonance Raman studies of quaternary structure of hemoglobin using a tryptophan beta 37 mutant.

Environmental changes of tyrosine and tryptophan residues of hemoglobin (Hb) upon its T to R transition of quaternary structure were investigated with ultraviolet resonance Raman (UVRR) spectroscopy excited at 235 nm. DeoxyHb A (T-form) showed a UVRR spectrum distinctly different from those of the ligated Hbs (R-form) including oxyHb, COHb, and metHb A, whereas the ligated Hbs exhibited similar UVRR spectra irrespective of the ligand species and the oxidation state of the heme. To characterize the spectral change of Trp-beta 37 at the alpha 1 beta 2 interface due to the quaternary structure transition, the UVRR spectra of Hb A were compared with the corresponding spectra of Hb Hirose (Trp-beta 37-->Ser). A difference spectrum between deoxyHb A and deoxyHb Hirose showed only Trp resonance Raman (RR) bands, which were reasonably ascribed to Trp-beta 37 in deoxyHb A. RR bands at 873 cm-1 (W17) and at 1360 and 1343 cm-1 (W7, Fermi doublet) indicated that the indole ring of Trp-beta 37 in deoxyHb A formed a strong hydrogen bond at the N1H site in hydrophobic environments. Tyr residues in deoxyHb Hirose seemed to be in the same environments as those of deoxyHb A. In contrast, the difference spectrum between Hb A and Hb Hirose in the ligated state displayed peaks for RR bands of both Trp and Tyr. The difference spectra were unaltered by the addition of 5 mM inositol hexaphosphate. This means that the differences were not caused by the tetramer to dimer dissociation but by a conformation change within a tetramer. Comparison of the Hb A-Hb Hirose difference spectra in the oxy and deoxy states revealed that the oxygenation-induced changes of Trp RR bands arose mostly from Trp-beta 37 with the small portion of remaining changes coming from Trp-beta 15, demonstrating that Trp-beta 37 plays a pivotal role in the quaternary structural change in Hb A.

Amino Acid Sequence↗
PubMed1993

Ultraviolet resonance Raman spectra of pea intact, large, and small phytochromes: differences in molecular topography of the red- and far-red-absorbing forms.

Ultraviolet resonance Raman (UV RR) spectra excited at 244 nm were observed for pea intact, large, and small phytochromes at pH 7.8. Raman bands assignable to Trp residues dominated the UV RR spectra. The intensity ratios of Trp W7 doublet bands, I(1358)/I(1342), of all three phytochromes in the red light-absorbing form (Pr) were almost the same as that of an aqueous Trp solution, indicating that most of the six and four Trp residues in the 59-kDa chromophoric and the C-terminal 59-kDa nonchromophoric domains, respectively, reside in hydrophilic microenvironments in Pr. This ratio increased under red light illumination, where photoequilibria are attained between Pr and the far-red-absorbing form (Pfr) for intact and small phytochromes and among Pr, a bleached intermediate (Ibl), and Pfr for large phytochromes. The increase of the intensity ratio was most prominent for small phytochromes. These observations suggest that the microenvironments around some Trp residues become more hydrophobic due to conformational changes induced by phototransformation from Pr to Ibl and that the hydrophobicity increase occurs mainly in the chromophoric domain. Among the six Trp residues in the chromophoric domain, Trp365 and Trp567 are likely candidates for those involved in this hydrophobicity increase. The intensity distribution of the amide I band shows little beta-sheet in both Pr and Pfr of the intact, large, and small phytochromes and indicates that alpha-helices and nonregular structure are less populated in the chromophoric domain than in the N-terminal 6-kDa segment and the C-terminal nonchromophoric domain.

Fabaceae↗
PubMed1992

Resonance Raman study on the active-site structure of a cooperative hemerythrin.

Resonance Raman spectra were observed for the oxy and azidomet forms of a cooperative hemerythrin (Hr) isolated from Lingula unguis and a noncooperative Hr from Siphonosoma cumanense. The O-O stretching frequency of the oxy derivative of the L. unguis Hr was lower in the high-affinity form generated at pH 7.6 than in the low-affinity form generated at pH 6.2, while that of the S. cumanense Hr did not change at those two pH values. The Fe-O-Fe symmetric stretching mode of L. unguis azidomet-Hr exhibited a frequency shift between pH 7.6 and 6.2, while that of S. cumanense was not shifted. However, the corresponding band of the oxy form did not show a pH-dependent frequency change. Therefore, it is noted that the azidomet form is not a suitable model for studying a mechanism of cooperativity, contrary to the structural similarity between the oxy and azidomet forms. The Fe-O2 as well as Fe-N3 stretching frequencies were found to have no relation with the oxygen affinity. Upon exchange of solvent from H2O to D2O, the O-O and Fe-O2 stretching modes of L. unguis Hr were shifted to higher and lower frequencies, respectively, and their magnitudes were the same for the high- and low-affinity forms. The same frequency shifts were observed for S. cumanense Hr.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗