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Y Shichida

Publications and source records attributed to Y Shichida.

At least 37 records · Page 2Linked to original sources
PubMed1999

Effect of anion binding on iodopsin studied by low-temperature fourier transform infrared spectroscopy.

The effect of anion binding on iodopsin, the chicken red-sensitive cone visual pigment, was studied by measurements of the Fourier transform infrared spectra of chloride- and nitrate-bound forms of iodopsin at 77 K. In addition to the blue shift of the absorption maximum upon substituting nitrate for chloride, the C=C stretching vibrations of iodopsin and its photoproducts were upshifted 5-6 cm(-)(1). The C=NH and C=ND stretching vibrations were the same in wavenumber between the chloride- and nitrate-bound forms, indicating that the binding of either chloride or nitrate has no effect on the interaction between the protonated Schiff base and the counterion. The vibrational bands of iodopsin in the fingerprint and the hydrogen out-of-plane wagging regions were insensitive to anion substitution, suggesting that local chromophore interactions with the anions are not crucial for the absorption spectral shift. In contrast, bathoiodopsin in the chloride-bound form exhibited an intense C(14)H wagging mode, whose intensity was considerably weakened upon substitution of nitrate for chloride. These results suggest that binding of chloride changes the environment near the C(14) position of the chromophore, which could be one of the factors in the thermal reverse reaction of bathoiodopsin to iodopsin in the chloride-bound form.

Anions↗
PubMed1999

Structural change of threonine 89 upon photoisomerization in bacteriorhodopsin as revealed by polarized FTIR spectroscopy.

The all-trans to 13-cis photoisomerization of the retinal chromophore of bacteriorhodopsin occurs selectively, efficiently, and on an ultrafast time scale. The reaction is facilitated by the surrounding protein matrix which undergoes further structural changes during the proton-transporting reaction cycle. Low-temperature polarized Fourier transform infrared difference spectra between bacteriorhodopsin and the K intermediate provide the possibility to investigate such structural changes, by probing O-H and N-H stretching vibrations [Kandori, Kinoshita, Shichida, and Maeda (1998) J. Phys. Chem. B 102, 7899-7905]. The measurements of [3-18O]threonine-labeled bacteriorhodopsin revealed that one of the D2O-sensitive bands (2506 cm(-1) in bacteriorhodopsin and 2466 cm(-1) in the K intermediate, in D2O exhibited 18(O)-induced isotope shift. The O-H stretching vibrations of the threonine side chain correspond to 3378 cm(-1) in bacteriorhodopsin and to 3317 cm(-1) in the K intermediate, indicating that hydrogen bonding becomes stronger after the photoisomerization. The O-H stretch frequency of neat secondary alcohol is 3340-3355 cm(-1). The O-H stretch bands are preserved in the T46V, T90V, T142N, T178N, and T205V mutant proteins, but diminished in T89A and T89C, and slightly shifted in T89S. Thus, the observed O-H stretching vibration originates from Thr89. This is consistent with the atomic structure of this region, and the change of the S-H stretching vibration of the T89C mutant in the K intermediate [Kandori, Kinoshita, Shichida, Maeda, Needleman, and Lanyi (1998) J. Am. Chem. Soc. 120, 5828-5829]. We conclude that all-trans to 13-cis isomerization causes shortening of the hydrogen bond between the OH group of Thr89 and a carboxyl oxygen atom of Asp85.

Aspartic Acid↗
PubMed1999

Amino acid residues controlling the properties and functions of rod and cone visual pigments.

The visual transduction processes in rod and cone photoreceptor cells are initiated by photon absorption by the different types of visual pigments. In relation to the functional difference between these cells, cone visual pigments in chicken retinas exhibit faster regeneration from 11-cis-retinal and opsin and faster decay of physiologically active intermediate (Meta II) than rod visual pigment, rhodopsin. Replacement of the amino acid residue at position 122 of chicken rhodopsin by the residues present in the respective cone pigments dramatically changes both the decay rate of Meta II and the rate of regeneration into those of the cone pigment-type, indicating that the residue at this position is a major determinant controlling these properties. Thus, the single replacement of amino acid residue at this position would be one of the key steps of the divergence into twilight and daylight vision.

Amino Acids↗
PubMed1999

Probing for the threshold energy for visual transduction: red-shifted visual pigment analogs from 3-methoxy-3-dehydroretinal and related compounds.

While azulenic retinal analogs failed to yield a red-shifted visual pigment analog, the 9-cis isomers of the push-pull polyenals 3-methoxy-3-dehydroretinal and 14F-3-methoxy-3-dehydroretinal yielded iodopsin pigment analogs with absorption maxima at, respectively, 663 and 720 nm. The former gave a relatively stable batho product (700 nm) and was able to activate transducin. A lower activity was observed for the latter. One possible explanation for the combined results is that the excitation energies of these red-shifted pigments are approaching the threshold energy for visual transduction (although at this time we cannot rigorously exclude a role of the added F-atom in reducing the transducin activity).

Retinal Pigments↗
PubMed1998

The hydrogen-bonding network of water molecules and the peptide backbone in the region connecting Asp83, Gly120, and Glu113 in bovine rhodopsin.

Difference Fourier transform infrared spectra were recorded between mutants of rhodopsin and their batho products. The pigments studied were single and combined mutants of intramembrane residues of bovine rhodopsin: Asp83, Glu113, Gly120, Gly121, and Glu122. Previous studies [Nagata, T., Terakita, A., Kandori, H., Kojima, D., Shichida, Y., and Maeda, A. (1997) Biochemistry 36, 6164-6170] showed that one of the water molecules which undergoes structural changes in this process forms hydrogen bonds with Glu113 and the Schiff base, and that another water molecule is linked to this structure through the peptide backbone. The present results show that this water molecule is located at the place that is affected by the replacements of Asp83 and Gly120 but only slightly by Gly121 and not at all by Glu122. Asp83 and Gly120 are close to each other, in view of the observations that the carboxylic C=O stretching vibration of Asp83 is affected by the G120A replacement and that each replacement affects the common peptide carbonyl groups. Our results suggest that these residues in the middle of helices B and C are linked-through a hydrogen-bonding network composed of water and the peptide backbone-with the region around Glu113.

Animals↗
PubMed1998

Selective activation of G-protein subtypes by vertebrate and invertebrate rhodopsins.

We have quantitatively investigated specificities in activating G-protein subtype by bovine and squid rhodopsins to examine whether or not the phototransduction cascade in each of the photoreceptor cells is determined by the colocalization of a large amount of G-protein subtype (Gt or Gq). In contrast to the efficient activation of respective Gt and Gq, bovine and squid rhodopsins scarcely activated G-protein counterparts. Exchange of alpha- and betagamma-subunits of Gt and Gq indicated the critical role of the alpha-subunit in specific binding to respective rhodopsins. Thus the specific recognition of G-protein subtype by each rhodopsin is a major mechanism in determining the phototransduction cascade.

Animals↗
PubMed1998

Identification of a new intermediate state that binds but not activates transducin in the bleaching process of bovine rhodopsin.

Using time-resolved low-temperature spectroscopy, we have examined whether or not bovine rhodopsin has a unique transducin-binding state, meta Ib, previously detected from chicken rhodopsin. Unlike chicken meta Ib, bovine meta Ib was detected only by detailed kinetics analysis of the bleaching process, but it was stabilized by transducin and visualized in the observed spectral changes. From the effect of GTPgammaS, it was revealed that meta Ib induced no GDP-GTP exchange reaction in transducin. Thus meta Ib is a common intermediate of vertebrate rhodopsin and transducin is activated in two steps by meta Ib and meta II.

Animals↗
PubMed1998

Visual pigment: G-protein-coupled receptor for light signals.

The visual pigment present in photoreceptor cells is a prototypical G-protein-coupled receptor (GPCR) that receives a light signal from the outer environment using a light-absorbing chromophore, 11-cis-retinal. Through cis-trans isomerization of the chromophore, light energy is transduced into chemical free energy, which is in turn utilized for conformational changes in the protein to activate the retinal G-protein. In combination with site-directed mutagenesis, various spectroscopic and biochemical studies identified functional residues responsible for chromophore binding, color regulation, intramolecular signal transduction and G-protein coupling. Extensive studies reveal that these residues are localized into specific domains of visual pigments, suggesting a highly manipulated molecular architecture in visual pigments. In addition to the recent findings on dysfunctional mutations in patients with retinitis pigmentosa or congenital night blindness, the mechanism of intramolecular signal transduction in visual pigments and their evolutionary relationship are discussed.

Amino Acid Sequence↗
PubMed1997

Presence of two rhodopsin intermediates responsible for transducin activation.

To identify how many rhodopsin intermediates interact with retinal G-protein transducin, the photobleaching process of chicken rhodopsin has been investigated in the presence or absence of transducin by means of time-resolved low-temperature spectroscopy. Singular value decomposition (SVD) analysis of the spectral data showed that a new intermediate called meta Ib is present between formally identified metarhodopsin I (now referred to as meta Ia) and metarhodopsin II (meta II). Since the absorption maximum of meta Ib (460 nm) is similar to that of meta Ia (480 nm), but considerably different from that of meta II (380 nm), meta Ib should have a protonated retinylidene Schiff base as its chromophore. Whereas transducin showed no effect on the conversion process between lumirhodopsin (lumi) and meta Ia, it affected the process between meta Ia and meta Ib and that between meta Ib and meta II. These results suggest that at least two intermediates (meta Ib and meta II) interact with transducin. The addition of GTPgammaS had no effect on the meta Ib-transducin interaction, while it abolished the ability of transducin to interact with meta II. Thus, meta Ib only binds to transducin, while meta II catalyzes a GDP-GTP exchange in transducin. These results suggest that deprotonation of the Schiff base chromophore is not necessary for the binding to transducin, while changes in protein structure including Schiff base deprotonation are needed to induce the GDP-GTP exchange in transducin.

Animals↗
PubMed1997

Photochemical and biochemical properties of chicken blue-sensitive cone visual pigment.

Through low-temperature spectroscopy and G-protein (transducin) activating experiments, we have investigated molecular properties of chicken blue, the cone visual pigment present in chicken blue-sensitive cones, and compared them with those of the other cone visual pigments, chicken green and chicken red (iodopsin), and rod visual pigment rhodopsin. Irradiation of chicken blue at -196 degrees C results in formation of a batho intermediate which then converts to BL, lumi, meta I, meta II, and meta III intermediates with the transition temperatures of -160, -110, -40, -20, and -10 degrees C. Batho intermediate exhibits an unique absorption spectrum having vibrational fine structure, suggesting that the chromophore of batho intermediate is in a C6-C7 conformation more restricted than those of chicken blue and its isopigment. As reflected by the difference in maxima of the original pigments, the absorption maxima of batho, BL, and lumi intermediates of chicken blue are located at wavelengths considerably shorter than those of the respective intermediates of chicken green, red and rhodopsin, but the maxima of meta I, meta II, and meta III are similar to those of the other visual pigments. These facts indicate that during the lumi-to-meta I transition, retinal chromophore changes its original position relative to the amino acid residues which regulate the maxima of original pigments through electrostatic interactions. Using time-resolved low-temperature spectroscopy, the decay rates of meta II and meta III intermediates of chicken blue are estimated to be similar to those of chicken red and green, but considerably faster than those of rhodopsin. Efficiency in activating transducin by the irradiated chicken blue is greatly diminished as the time before its addition to the reaction mixture containing transducin and GTP increases, while that by irradiated rhodopsin is not. The time profile is almost identical with those observed in chicken red and green. Thus, the faster decay of enzymatically active state is common in cone visual pigments, independent of their spectral sensitivity.

Animals↗
PubMed1997

A novel Go-mediated phototransduction cascade in scallop visual cells.

Scallop retinas contain ciliary photoreceptor cells that respond to light by hyperpolarization like vertebrate rods and cones, but the response is generated by a different phototransduction cascade from those of rods and cones. To elucidate the cascade, we investigated a visual pigment and a G-protein functioning in the hyperpolarizing cell. Sequencing of cDNAs and in situ hybridization experiments showed that the hyperpolarizing cells express a novel subtype of visual pigment, which showed significant differences in amino acid sequence from other visual pigments. Cloning cDNA genes of G-protein and immunohistochemical analysis revealed the presence of an alpha subunit of a Go type G-protein, 83% identical in amino acid sequence to mammalian Go(alpha) in the nervous system, in the photoreceptive region of the cells. The results demonstrate that a novel, Go-mediated, phototransduction cascade is present in the hyperpolarizing cells. The phototransduction cascade in the scallop hyperpolarizing cell provides an alternative system to investigate Go-mediated transduction pathways in the nervous system. Molecular phylogenetic analysis strongly suggests that the Go-mediated phototransduction system emerged before the divergence of animals into vertebrate and invertebrate in the course of evolution.

Amino Acid Sequence↗
PubMed1997

Water and peptide backbone structure in the active center of bovine rhodopsin.

Difference FTIR spectra in the conversion of rhodopsin or isorhodopsin to bathorhodopsin were recorded for recombinant wild-type and E113Q bovine rhodopsins. Differences in various vibrational modes between E113Q and the wild-type proteins whose Schiff bases interact with chloride and Glu113, respectively, were analyzed. Water molecules in rhodopsin that change upon formation of bathorhodopsin are detected by a change in frequency of the O-H stretching vibration from 3538 to 3525 cm(-1). This change in the wild-type protein is absent in E113Q. One or a few water molecules are therefore suggested to be located in the proximity of Glu113, the counterion of the Schiff base. Another water vibration at 3564 cm(-1), which is shifted to 3542 cm(-1) in bathorhodopsin in the wild type, persists in E113Q but with approximately 5-cm(-1) shift toward higher frequency. This is due to water molecules that may be located at a site somewhat more remote from Glu113. Structural changes of some peptide carbonyls and amides are also absent in E113Q. On the other hand, the E113Q protein shows shifts of the N-H+ stretching vibrational band, that is probably due to the protonated Schiff base, upon conversion of rhodopsin to bathorhodopsin. No corresponding changes were observed in the wild type. We propose a model in which a water molecule interacts with Glu113, the protonated Schiff base, and peptide carbonyls, and amides. These residues undergo structural changes upon formation of bathorhodopsin.

Animals↗
PubMed1997

Single amino acid residue as a functional determinant of rod and cone visual pigments.

The visual transduction processes in rod and cone photoreceptor cells begin with photon absorption by the different types of visual pigments. Cone visual pigments exhibit faster regeneration from 11-cis-retinal and opsin and faster decay of physiologically active intermediate (meta II) than does the rod visual pigment, rhodopsin, as expected, due to the functional difference between rod and cone photoreceptor cells. To identify the amino acid residue(s) responsible for the difference in molecular properties between rod and cone visual pigments, we selected three amino acid positions (64, 122, and 150), where cone visual pigments have amino acid residues electrically different from those of rhodopsin, and prepared mutants of rhodopsin and chicken green-sensitive cone visual pigment. The results showed that the replacement of Glu-122 of rhodopsin by the residue containing green- or red-sensitive cone pigment converted rhodopsin's rates of regeneration and meta II decay into those of the respective cone pigments, whereas the introduction of Glu-122 into green-sensitive cone visual pigment changed the rates of these processes into rates similar to those of rhodopsin. Furthermore, exchange of the residue at position 122 between rhodopsin and chicken green-sensitive cone pigment interchanges their efficiencies in activating retinal G protein transducin. Thus, the amino acid residue at position 122 is a functional determinant of rod and cone visual pigments.

Animals↗
PubMed1996

Chromophore configuration of iodopsin and its photoproducts formed at low temperatures.

The photochemical reactions of iodopsin at low temperatures were investigated by a combination of absorption spectroscopy and chromophore extraction to show the formation of isomeric photoproducts other than the all-trans intermediates. We first confirmed that the chromophore in iodopsin is an 11-cis-retinal. Next, iodopsin samples were irradiated with light of different wavelengths at selected temperatures ranging from -190 to 0 degrees C, and their retinylidene chromophores were extracted as oximes after warming the sample to 0 degree C. The isomeric composition of the extracted chromophores was analyzed by high-performance liquid chromatography. It was confirmed that bathoiodopsin produced at -190 degrees C has an all-trans chromophore, but a considerable amount of its chromophore thermally reisomerizes to the 11-cis form upon warming. Photoproducts formerly assigned as lumi- and metaiodopsins [Yoshizawa, T., & Wald, G. (1967) Nature 214, 566-571; Hubbard, R., & Kropf, A. (1959) Nature 183, 448-450] were produced by extensive irradiation of iodopsin at -80 and -40 degrees C, respectively, with red light, but their chromophores were identified to be 7-cis-retinals instead of all-trans-retinals. Thus these photoproducts are artificial byproducts formed as a result of photon absorption by all-trans intermediates. The absorption spectrum of the 7-cis product formed from bovine rhodopsin shows no spectral shift when it is warmed from -80 to 0 degrees C, but the spectrum of 7-cis species formed from iodopsin shifted about 40 nm to the blue at a transition temperature of -60 degrees C. This result indicates a unique chromophore-opsin interaction in iodopsin. Four all-trans intermediates of iodopsin were identified above -80 degrees C under irradiation conditions in which no 7-cis products accumulated. Their absorption maxima were estimated to be approximately 570, approximately 530, approximately 470, and approximately 380 nm. These species should correspond to BL-iodopsin, lumiiodopsin, metaiodopsin I, and metaiodopsin II, respectively, assigned by room temperature laser photolysis [Shichida, Y., Okada, T., Kandori, H., Fukada, Y., & Yoshizawa, T. (1993) Biochemistry 32, 10832-10838].

Animals↗
PubMed1996

Structure around C6-C7 bond of the chromophore in bathorhodopsin: low-temperature spectroscopy of 6s-cis-locked bicyclic rhodopsin analogs.

To elucidate the structural changes near the beta-ionone ring region of the chromophore during the photobleaching process of rhodopsin, the photochemical and subsequent thermal reactions of rhodopsin analogs, whose retinylidene chromophores were fixed in a 6s-cis form with a five-membered ring (6,5-rhodopsin) and a seven-membered ring (6,7-rhodopsin), respectively, were investigated by low-temperature spectroscopy. Like rhodopsin, both the rhodopsin analogs convert to the respective batho-intermediates upon absorption of light at -190 degrees C. The extinction coefficient of batho-intermediate of 6,5-rhodopsin is similar to that of bathorhodopsin, while that of 6,7-rhodopsin is considerably smaller than that of bathorhodopsin. Like bathorhodopsin, the batho-intermediate of 6,5-rhodopsin directly converts to lumi-intermediate, while that of 6,7-rhodopsin first converts to a blue-shifted intermediate and then to lumi-intermediate. These results strongly suggest that the structure around the beta-ionone ring region of the bathorhodopsin chromophore resembles 6,5-retinal rather than 6,7-retinal. From the comparison of the structural features among retinal, 6,5-retinal, and 6,7-retinal, a possible conformation around C6-C7 bond of the bathorhodopsin chromophore is discussed.

Animals↗
PubMed1996

Molecular properties of chimerical mutants of gecko blue and bovine rhodopsin.

In spite of the high similarity in amino acid sequence between rod visual pigment rhodopsin and gecko blue-sensitive pigment (gecko blue), not only the spectral sensitivities but also the thermal decay rates of the meta II- and III-intermediates are noticeably different from one another [Kojima et al. (1995) Biochemistry 34, 1096-1106]. In order to identify the protein region(s) that contain(s) key residue being responsible for the functional difference, we constructed six chimerical mutants derived from gecko blue and bovine rhodopsin, with the aid of protein production in a human embryonic kidney cell line (293S). While the absorption maximum of every mutant was located in between gecko blue (466 nm) and bovine rhodopsin (500 nm), a large blue-shift (18 nm) was observed when the helices I-III of rhodopsin were replaced with those of gecko blue. A time resolved spectroscopic study demonstrated that this replacement also accelerated the decay rate of the meta II-intermediate. The decay of the meta III-intermediate of the mutants became faster as the compartment of gecko blue was increased. Thus, the faster decay of the meta II-intermediate of gecko blue is largely attributed to residues within helices I-III, while the decay of the meta III-intermediate apparently depends on the overall structure of the protein.

Animals↗