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Y Shichida

Publications and source records attributed to Y Shichida.

At least 55 records · Page 3Linked to original sources
PubMed1995

Effect of chloride on the thermal reverse reaction of intermediates of iodopsin.

Among the intermediates in the bleaching process of iodopsin, a chicken red-sensitive cone visual pigment, the batho and meta I intermediates (batho and meta I) formed at low temperatures revert to the original iodopsin by thermal reactions [Yoshizawa & Wald (1967) Nature 214, 566-571; Imamoto, Imai, Yoshizawa, & Shichida (1994) FEBS Lett. 354, 165-168]. In order to elucidate the relationship between Cl- binding to iodopsin and these reverse reactions, we have prepared a sample of iodopsin whose Cl(-)-binding site is vacant (anion-unbound iodopsin) and compared the thermal reactions of its batho and meta I intermediates with those of Cl(-)-bound (native) and nitrate-bound iodopsins. The reverse reaction from batho is observed in both Cl(-)-bound and anion-unbound iodopsins, while the reaction from meta I is observed only in Cl(-)-bound iodopsin. These results indicate that Cl- binding is indispensable for the reverse reaction from meta I, but not from batho. The reverse reaction from meta I has been further investigated as a function of Cl- concentration, and the dissociation constant of Cl- in meta I is estimated to be approximately 20 mM. This value is about 200 times larger than that of iodopsin (0.1 mM), and close to the physiological Cl- concentration in photoreceptor cells, suggesting that Cl- could be released from the protein moiety during the bleaching of iodopsin.

Animals↗
PubMed1995

Difference in molecular properties between chicken green and rhodopsin as related to the functional difference between cone and rod photoreceptor cells.

Using low-temperature spectroscopy, we have investigated the photobleaching process of chicken green, a green-sensitive cone visual pigment present in chicken retina, and compared it to that of rhodopsin, a rod visual pigment. Like rhodopsin, chicken green converts to all-trans-retinal and opsin through batho, lumi, and meta I, II, and III intermediates. However, all of the intermediates of chicken green except lumi, are less stable than the corresponding intermediates of rhodopsin. While early intermediates, batho and lumi are similar in absorption maxima between chicken green and rhodopsin, the meta intermediates of chicken green are about 20 nm blue shifted from those of rhodopsin. Low-temperature time-resolved spectroscopy was applied to estimate the thermodynamic properties of meta intermediates, and it indicated that the less stable properties of meta II and III intermediates of chicken green originate from the smaller activation enthalpies. The decay of the meta II intermediate of chicken green is greatly suppressed when a chicken green sample is irradiated at alkaline conditions while the net charge becomes similar to that of rhodopsin at neutral conditions. These results strongly suggest that the functional properties of chicken green that are different from those of rhodopsin are regulated by the dissociative amino acid residue(s).

Avian Proteins↗
PubMed1995

Reason for the lack of light-dark adaptation in pharaonis phoborhodopsin: reconstitution with 13-cis-retinal.

The reconstitution of pharaonis phoborhodopsin was performed by incubation of its opsin with 13-cis-retinal. Spectrum change was very slow, and two phases of the change were observed: the first and second phases are due to the transient formation of 13-cis pigment and spontaneous isomerization to all-trans-retinal, respectively. Slow binding supports an idea that the retinal binding pocket of ppR is highly restricted. Being bent in the configuration, 13-cis-retinal cannot be accommodated in the pocket due to the steric hindrance. This is a possible reason for the lack of light-dark adaptation.

Archaeal Proteins↗
PubMed1995

Purification and low temperature spectroscopy of gecko visual pigments green and blue.

We purified two kinds of visual pigments, gecko green and gecko blue, from retinas of Tokay geckos (Gekko gekko) by two steps of column chromatography, and investigated their photobleaching processes by means of low temperature spectroscopy. Absorption maxima of gecko green and blue solubilized in a mixture of 3-[(3-cholamidopropyl)dimethylammonio]-1- propanesulfonate (CHAPS) and phosphatidylcholine were 522 and 465 nm, respectively, which are close to those observed in the photoreceptor cells. Low temperature spectroscopy identified six intermediates in the photobleaching process of gecko green; batho (lambda max = 569 nm), BL (lambda max = 519 nm), lumi (507 nm), meta I (approximately 486 nm), meta II (approximately 384 nm), and meta III intermediates (approximately 500 nm). In contrast to the high similarity in amino acid sequence between gecko green and iodopsin [Kojima, D., et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 6841-6845], the batho-green did not revert thermally to original gecko green but converts to the next intermediate. The photobleaching process of gecko blue was investigated by low temperature spectroscopy, and three intermediates, meta I (lambda max = approximately 470 nm), meta II (lambda max = approximately 370 nm) and meta III (lambda max = approximately 475 nm), were identified. A comparative study on the thermal behavior of meta intermediates revealed that the thermal stability of meta II intermediate of both of the gecko visual pigments is lower than that of metarhodopsin II. The result supports the idea that both the gecko visual pigments are cone-type ones.

Animals↗
PubMed1994

Direct observation of the thermal equilibria among lumirhodopsin, metarhodopsin I, and metarhodopsin II in chicken rhodopsin.

Using low-temperature time-resolved spectroscopy, we have directly observed thermal back reaction of metarhodopsin I (meta I) to lumirhodopsin (lumi) and that of metarhodopsin II (meta II) to meta I in chicken rhodopsin to demonstrate the presence of thermal equilibria among lumi, meta I, and meta II. The back reaction from meta I to lumi was observed when the rhodopsin sample irradiated at -35 degrees C was warmed to -20 degrees C, while that from meta II to meta I was observed when the sample irradiated at -10 degrees C was cooled to -20 degrees C. Thermodynamic parameters of lumi, meta I, and meta II were calculated from the equilibrium constants estimated by analyzing the spectra of the equilibrium states at temperatures ranging from -30 to -10 degrees C. The results showed that meta I has an enthalpy and an entropy considerably smaller than those of lumi and meta II, while the difference in thermodynamic parameters between lumi and meta II is not so large. These results suggest that meta I is a crucial stage of conversion of the light energy captured by the chromophore into restricted conformations of the chromophore and/or protein, from which a large conformational change of the protein starts to form meta II.

Animals↗
PubMed1994

Thermal recovery of iodopsin from its meta I-intermediate.

The thermal reaction of meta I-intermediate of iodopsin (metaiodopsin I), a chicken red-sensitive cone pigment, was studied by low-temperature spectrophotometry at -20 degrees C. Irradiation of iodopsin at -20 degrees C produced metaiodopsin I, whose absorption maximum was at about 470 nm. An incubation of metaiodopsin I at -20 degrees C resulted in a conversion to metaiodopsin II having absorption maximum at about 380 nm, as well as a concurrent formation of a red-shifted product stable at room temperature. Since the absorption spectrum and photo-reactivity of the red-shifted product were identical with those of iodopsin, the red-shifted product should be iodopsin. Thus a part of metaiodopsin I can revert to iodopsin by the thermal reaction unlike metarhodopsin I.

Animals↗
PubMed1994

Is chicken green-sensitive cone visual pigment a rhodopsin-like pigment? A comparative study of the molecular properties between chicken green and rhodopsin.

Chicken green is a visual pigment present in chicken green-sensitive cones and has an amino acid sequence more similar than any other cone visual pigments to the rod visual pigments, rhodopsins. Here we have investigated the molecular properties of chicken green and compared them with those of rhodopsin to elucidate whether or not chicken green is a rhodopsin-like pigment. While chicken green has a molecular extinction coefficient and a photosensitivity very similar to those of rhodopsin, it displays faster regeneration from 11-cis-retinal and opsin and faster formation and decay of the physiologically active meta II intermediate than rhodopsin. These differences correlate with the physiological difference between cones and rods. Thus in spite of the similarity in amino acid sequence, chicken green displays molecular properties required for a cone visual pigment that are clearly different from those of rhodopsin.

Animals↗
PubMed1994

Circular dichroism of metaiodopsin II and its binding to transducin: a comparative study between meta II intermediates of iodopsin and rhodopsin.

Through low-temperature absorption and circular dichroism (CD) spectroscopies, and G-protein (transducin) binding experiments, we have investigated molecular properties of the meta II intermediate of iodopsin, a cone visual pigment present in chicken red-sensitive cones. The meta II intermediate of iodopsin (metaiodopsin II, lambda max = 390 nm) displayed a positive CD band at about 390 nm and a large negative CD band below 300 nm. It dissociated into all-trans-retinal and the protein moiety. A long-lived intermediate corresponding to the meta III intermediate of rhodopsin was not observed in iodopsin, under our experimental conditions. Decay of metaiodopsin II was significantly suppressed in the presence of transducin, but not in the presence of both transducin and GTP, indicating that metaiodopsin II can interact with transducin and activate it. Both metaiodopsin II and metarhodopsin II displayed a large negative CD band below 300 nm. This fact suggested that during the formation of both meta II intermediates, some aromatic amino acid residues and/or a disulfide bond are rearranged, which may be important for expression of catalytic activity for exchange of GDP to GTP on transducin. On the other hand, metaiodopsin II decayed more than 10 times faster than metarhodopsin II. This fact may be one of the reasons why cones are less photosensitive than rods.

Animals↗
PubMed1994

Spectroscopic observation of the intramolecular electron transfer in the photoactivation processes of nitrile hydratase.

The photoactivation phenomena of the photosensitive enzyme nitrile hydratase (NHase) was studied by various spectroscopic methods. We have already shown that the photoactivation of NHase accompanies oxidation of an iron atom in the NHase [Honda et al. (1992) FEBS Lett. 301, 177-180]. From the results obtained in the present study by absorption, action, and fluorescence spectra, we show that the chromophore responsible for the photoactivation process is the iron complex, and the tryptophan residues in NHase induce the oxidation of the iron atom via an energy-transfer process. The nanosecond flash photolysis experiment revealed that this photoactivation process is completed within 50 ns, which suggests that the changes observable in the absorption spectra originate from an intramolecular electron transfer occurring from an electronically excited state. Also the role of a stabilizing reagent, namely, n-butyric acid (BA), was investigated using the above methods, which revealed that BA, besides its stabilizing effect, contributes to the increase in apparent photoactivation rate.

Butyrates↗
PubMed1994

What makes red visual pigments red? A resonance Raman microprobe study of retinal chromophore structure in iodopsin.

We have obtained resonance Raman spectra of iodopsin, a red-sensitive (lambda max 571 nm) pigment from chicken cone cells, to investigate the molecular mechanism of the opsin shift in visual pigments. Detergent-solubilized iodopsin samples were examined with a Raman microprobe to obtain spectra from a 77-K photostationary steady-state mixture composed of 11-cis-iodopsin and its 9-cis-isoiodopsin and all-trans-bathoiodopsin photoproducts. The vibrational modes of these species have been assigned by comparison with spectra of the corresponding bovine pigments. The single bond stretching frequencies of the bovine, toad, and chicken pigments are found to exhibit a regular correlation as a function of the pigment absorption maxima that is consistent with the expected effects of increased electron delocalization. The C = NH stretching frequencies of iodopsin and bathoiodopsin are at 1644 and 1638 cm-1, respectively, and shift down to 1621 and 1617 cm-1, respectively, when the nitrogen is deuterated. The C = ND stretching frequencies of the various pigments are found to decrease linearly with increasing absorption maxima, suggesting that at least part of the opsin shift in visual pigments results from weakened electrostatic interaction between the retinal chromophore and its protein counterion. The Raman data are inconsistent with the idea that a charged protein residue is shifted along the chromophore to regulate the opsin shift. Taken together with the mutagenesis and model compound results, these resonance Raman data suggest that the opsin shift between the green and red cone visual pigment arises from two effects. First, Tyr-274 provides increased electrostatic stabilization of the Schiff base-counterion ion pair. Second, the opsin shift is enhanced by the dipolar residues Ser-177 and Thr-282 that interact with the chromophore near the ionone ring to preferentially stabilize the highly dipolar charge distribution of the electronically excited retinal chromophore [Mathies, R., & Stryer, L. (1976) Proc. Natl. Acad. Sci. U.S.A. 73, 2169-2173].

Animals↗
PubMed1994

Visual pigments in the pineal complex of the Japanese quail, Japanese grass lizard and bullfrog: immunocytochemistry and HPLC analysis.

We investigated localization of visual pigments in the pineal complex of Japanese quail, Japanese grass lizards and bullfrogs immunocytochemically by use of the antiserum against bovine rhodopsin (Rh-As) and monoclonal antibodies against chicken iodopsin (Io-mAb). We also analyzed retinoids, chromophores of visual pigments, by a high performance liquid chromatography (HPLC). The outer segments and cell membranes of some photoreceptor cells in the pineal organ of the Japanese quail exhibited immunoreactivity to Rh-As, but there are also many immunonegative cells. The number of immunoreactive cells among individuals varied. Immunoreactivity to Io-mAb was weak or did not exist. The HPLC analysis revealed peaks of 11-cis and all-trans isomers of retinal in the oxime extracts of the pineal organ of Japanese quail and chickens. In the pineal of Japanese grass lizards, the outer segments of some cells were immunopositive to Io-mAb, but there were no cells immunoreactive to Rh-As. The parietal eye exhibited a well-developed lens and photoreceptor cells, but the outer segments of photoreceptor cells were immunonegative to both Rh-As and Io-mAb. In bullfrogs, three types of cells were identified in both the pineal and frontal organ; (1) immunopositive to Rh-As, (2) immunopositive to Io-mAb and (3) immunonegative to either of the antibodies. In the pineal organ of bullfrogs, 11-cis and all-trans retinal and 11-cis 3-dehydroretinal were detected, and 11-cis and all-trans retinal were also detected in the frontal organ. We detected 11-cis and all-trans retinal in the ventral part of diencephalon including the hypothalamus. Thus, the chromophore is the same between the retinal and pineal visual pigments, but the expression of opsins is different between the retina and pineal complex, which probably reflects the different function of each organ.

Animals↗
PubMed1994

Shape of the chromophore binding site in pharaonis phoborhodopsin from a study using retinal analogs.

To investigate the shape of the chromophore binding site of pharaonis phoborhodopsin (ppR), ppR-opsin was incubated with five ring-modified retinal analogs: an acyclic retinal, phenylretinal, alpha-retinal, cyclohexylretinal and 5-isopropyl-alpha-retinal. The experimental results were compared with those obtained from bacteriorhodopsin-opsin (bR-opsin) and the same retinal analogs. It was suggested that ring chain conformation is important in affecting the spectral shoulder unique for the absorption spectrum of ppR. The rate of pigment formation depended greatly on the analogs used with the planar analogs showing rapid formation. Thus, we concluded that the space of the retinal binding site of ppR is restricted to the plane of the cyclohexenyl ring of the chromophore, whereas that of bR is less restricted.

Archaeal Proteins↗
PubMed1993

Water structural changes in lumirhodopsin, metarhodopsin I, and metarhodopsin II upon photolysis of bovine rhodopsin: analysis by Fourier transform infrared spectroscopy.

Difference Fourier transform infrared spectra of lumirhodopsin, metarhodopsin I, and metarhodopsin II versus rhodopsin were recorded with hydrated films of bovine rod outer segments at 200, 240, and 270 K. In the region between 3700 and 3450 cm-1, the O-H stretching vibrational bands of water were identified by H(2)18O and 2H2O shifts. Lumirhodopsin and metarhodopsin I exhibit almost identical spectral shape in this region. The O-H stretching vibration band of water was detected at 3533 cm-1 upon formation of lumirhodopsin and metarhodopsin I and at 3641 cm-1 upon formation of metarhodopsin II. The results suggest that hydrogen bonding of water molecules in the protein is stronger in lumirhodopsin and metarhodopsin I, intermediates with a protonated Schiff base, than in metarhodopsin II with an unprotonated Schiff base. This is similar to the case of photoreaction of bacteriorhodopsin, in which stronger hydrogen bonding of water is formed in the L intermediate than the M intermediate [Maeda, A., Sasaki, J., Shichida, Y., & Yoshizawa, T. (1992) Biochemistry 31, 462-467].

Animals↗
PubMed1993

Nanosecond laser photolysis of iodopsin, a chicken red-sensitive cone visual pigment.

The photobleaching process of iodopsin (a chicken red-sensitive cone visual pigment) purified in a detergent system containing CHAPS and phosphatidylcholine was investigated by means of nanosecond laser photolysis at room temperature. Excitation of iodopsin with a nanosecond laser pulse (wavelength, 560 nm; pulse width, 17 ns) resulted in the formation of at least four intermediates on the nanosecond to millisecond time scale. The earliest intermediate detected had an absorption maximum at 571 nm, which was very close to that of original iodopsin (lambda max = 567 nm), and remarkably blue-shifted as compared with that of bathoiodopsin [lambda max = 625 nm; Kandori et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 8908-8912]. The intermediate, named BL-iodopsin, converted to the next intermediate, lumiiodopsin (lambda max = 535 nm), with a time constant of 130 ns. The BL intermediate had an absorption maximum just between batho- and lumiiodopsins, and an extinction coefficient comparable with these intermediates. These properties are different from those of the corresponding intermediate of rhodopsin [BL(BSI)-rhodopsin], suggesting that the binding of chloride to iodopsin, but not to rhodopsin, has an influence upon changes of the chromophore-opsin interaction in the early stage of photobleaching of iodopsin. Lumiiodopsin converted to metaiodopsin I (lambda max < 500 nm) with a time constant of 230 microseconds, and then to metaiodopsin II (lambda max = 390 nm) with a time constant of 6 ms. A thermal equilibrium between metaiodopsin I and II was established, but unlike meta intermediates of rhodopsin, they showed little temperature dependence.

Animals↗
PubMed1993

Photoisomerization mechanism of the rhodopsin chromophore: picosecond photolysis of pigment containing 11-cis-locked eight-membered ring retinal.

The primary photochemical event in rhodopsin is an 11-cis to 11-trans photoisomerization of its retinylidene chromophore to form the primary intermediate photorhodopsin. Earlier picosecond studies have shown that no intermediate is formed when the retinal 11-ene is fixed through a bridging five-membered ring, whereas a photorhodopsin-like intermediate is formed when it is fixed through a flexible seven-membered ring. Results from a rhodopsin analog formed from a retinal with locked 11-ene structure through the more flexible eight-membered ring (Ret8) are described. Incubation of bovine opsin with Ret8 formed two pigments absorbing at 425 nm (P425) and 500 nm (P500). P425, however, is an artifact because it formed from thermally denatured opsin or other proteins and Ret8. Excitation of P500 with a picosecond green pulse led to formation of two intermediates corresponding to photo- and bathorhodopsins. These results demonstrate that an appearance of early intermediates is dependent on the flexibility of the 11-ene and that the photoisomerization of P500 proceeds by stepwise changes of chromophore-protein interaction, which in turn leads to a relaxation of the highly twisted all-trans-retinylidene chromophore in photorhodopsin.

Animals↗
PubMed1993

Identification of the alpha-subunits of rod and cone transducin in chicken photoreceptor cells.

The chicken retina has several types of cone photoreceptor cells, each of which contains a visual pigment, chicken red (iodopsin), green, blue or violet. Although biochemical and photochemical properties of these cone pigments have been well characterized, no information is available about the chicken photoreceptor G-protein, transducin, which couples with the visual pigment to convert a photon signal into a cellular response. To identify alpha-subunits of chicken rod and cone transducins (Tr alpha and Tc alpha, respectively), we produced two site-directed antibodies which discriminate between bovine Tr alpha and Tc alpha. Immunohistochemical studies on chicken retinas revealed that the antibody against bovine Tr alpha specifically stained the rod outer segments. On the other hand, the antibody against bovine Tc alpha uniformly stained the outer segments of the double cones and all types of single cones, while the single cones were immunohistochemically classified into three types by using a combination of antibodies against bovine rhodopsin and chicken iodopsin. Immuno-blot analyses demonstrated that the antibody against Tc alpha recognized a single band of chicken photoreceptor protein, whose molecular weight (42,000) was in good agreement with that of bovine Tc alpha (41,000). The antibody against Tr alpha recognized a protein having the same molecular weight as that of bovine Tr alpha (39,000). These observations strongly suggested that all types of chicken cone cells have a single common Tc alpha (42 kDa) structurally related to bovine Tc alpha, though each cone cell type has a distinct visual pigment.

Animals↗
PubMed1992

Protein changes associated with reprotonation of the Schiff base in the photocycle of Asp96-->Asn bacteriorhodopsin. The MN intermediate with unprotonated Schiff base but N-like protein structure.

The difference Fourier transform infrared spectrum for the N intermediate in the photoreaction of the light-adapted form of bacteriorhodopsin can be recorded at pH 10 at 274 K (Pfefferlé, J.-M., Maeda, A., Sasaki, J., and Yoshizawa, T. (1991) Biochemistry 30, 6548-6556). Under these conditions, Asp96-->Asn bacteriorhodopsin gives a photoproduct which shows changes in protein structure similar to those observed in N of wild-type bacteriorhodopsin. However, decreased intensity of the chromophore bands and the single absorbance maximum at about 400 nm indicate that the Schiff base is unprotonated, as in the M intermediate. This photoproduct was named MN. At pH 7, where the supply of proton is not as restricted as at pH 10, Asp96-->Asn bacteriorhodopsin yields N with a protonated Schiff base. The Asn96 residue, which cannot deprotonate as Asp96 in wild-type bacteriorhodopsin, is perturbed upon formation of both MN at pH 10 and N at pH 7. We suggest that the reprotonation of the Schiff base is preceded by a large change in the protein structure including perturbation of the residue at position 96.

Asparagine↗