Research Topics
Genomes and Genes | Yoshinori ShichidaSummaryAffiliation: Kyoto University Country: Japan Publications
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Publications
Evolution of opsins and phototransductionYoshinori Shichida
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Philos Trans R Soc Lond B Biol Sci 364:2881-95. 2009..We will show how the advances in molecular biology and biophysics have given us insights into how evolution works at the molecular level...
Amino acid residues responsible for the meta-III decay rates in rod and cone visual pigmentsShigeki Kuwayama
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, and CREST, Japan Science and Technology Agency, Kyoto, Japan
Biochemistry 44:2208-15. 2005....- Covalent bond between ligand and receptor required for efficient activation in rhodopsinTake Matsuyama
Department of Biophysics, Graduate School of Science and CREST JST, Kyoto University, Kyoto 606 8502, Japan
J Biol Chem 285:8114-21. 2010.... - Photochemical nature of parietopsinKazumi Sakai
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 51:1933-41. 2012..Thus, parietopsin behaves as an "evolutionary intermediate" between invertebrate and vertebrate visual opsins... - Expression and comparative characterization of Gq-coupled invertebrate visual pigments and melanopsinAkihisa Terakita
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
J Neurochem 105:883-90. 2008..Our findings are also important in that this is the first report describes a heterologous large-scale expression of the Gq-coupled invertebrate visual pigments in cultured cells... - Cephalochordate melanopsin: evolutionary linkage between invertebrate visual cells and vertebrate photosensitive retinal ganglion cellsMitsumasa Koyanagi
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
Curr Biol 15:1065-9. 2005..The cephalochordate rhabdomeric photoreceptor represents an evolutionary link between the invertebrate visual photoreceptor and the vertebrate circadian photoreceptor... - A pivot between helices V and VI near the retinal-binding site is necessary for activation in rhodopsinsHisao Tsukamoto
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
J Biol Chem 285:7351-7. 2010.... 
Comparative studies on the late bleaching processes of four kinds of cone visual pigments and rod visual pigmentKeita Sato
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 51:4300-8. 2012..These results strongly suggest that rhodopsin and S, M1, and M2 cone visual pigments share a molecular mechanism for activation, whereas the L-group pigment may have a special reaction mechanism involving the chloride-binding site...- Photoisomerization efficiency in UV-absorbing visual pigments: protein-directed isomerization of an unprotonated retinal Schiff baseKei Tsutsui
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 46:6437-45. 2007..These results suggest that the mouse UV pigment has a specific mechanism for the efficient photoisomerization of its unprotonated Schiff base chromophore... - Generation of knock-in mice carrying third cones with spectral sensitivity different from S and L conesAkishi Onishi
Department of Biophysics, Graduate School of Science, Kyoto University, Japan
Zoolog Sci 22:1145-56. 2005.... - Conformational change of the transmembrane helices II and IV of metabotropic glutamate receptor involved in G protein activationTakahiro Yamashita
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
J Neurochem 106:850-9. 2008..These results provided the model that the conformational changes at the cytoplasmic ends of helices II and IV of mGluR are involved in the efficient G protein coupling... - Direct observation of the complex formation of GDP-bound transducin with the rhodopsin intermediate having a visible absorption maximum in rod outer segment membranesTakefumi Morizumi
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, and CREST, Japan Science and Technology Agency, Japan
Biochemistry 44:9936-43. 2005..Our results strongly suggest that the protein conformational change of the rhodopsin intermediate after binding to Gt is important for the induction of the nucleotide release from the alpha-subunit of Gt... - Functional analysis of the second extracellular loop of rhodopsin by characterizing split variantsKazumi Sakai
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
Photochem Photobiol Sci 9:1490-7. 2010..These results suggest that ECL2 'mechanically' drives the conformational change of rhodopsin... - A rhodopsin exhibiting binding ability to agonist all-trans-retinalHisao Tsukamoto
Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606-8502, Japan
Proc Natl Acad Sci U S A 102:6303-8. 2005..In addition, an additional mechanism was acquired in vertebrate rhodopsin to prevent completely the binding of exogenous all-trans-retinal during molecular evolution... - Two isoforms of chicken melanopsins show blue light sensitivityMasaki Torii
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
FEBS Lett 581:5327-31. 2007..The melanopsin isoforms found in this study may function as pineal circadian photoreceptors... - Mechanism of G-protein activation by rhodopsinYoshinori Shichida
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, CREST, Japan Science and Technology Agency, Japan
Photochem Photobiol 83:70-5. 2007..Thus, the GDP-GTP exchange reaction, namely G-protein activation, by rhodopsin proceeds through at least two steps, with conformational changes in both rhodopsin and the G-protein... - Direct observation of the pH-dependent equilibrium between metarhodopsins I and II and the pH-independent interaction of metarhodopsin II with transducin C-terminal peptideKeita Sato
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 49:736-41. 2010..Therefore, there is no need for proton uptake by the protein moiety of opsin for the binding to the peptide... - Counterion displacement in the molecular evolution of the rhodopsin familyAkihisa Terakita
Department of Biophysics, Graduate School of Science, Kyoto University, and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606-8502, Japan
Nat Struct Mol Biol 11:284-9. 2004..Thus an ancestral vertebrate rhodopsin probably acquired the Glu113 counterion, followed by structural optimization for efficient G protein activation during molecular evolution... - G protein subtype specificity of rhodopsin intermediates metarhodopsin Ib and metarhodopsin IITakefumi Morizumi
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
Photochem Photobiol 85:57-62. 2009..These results suggested that meta-Ib is the state that exhibits specific interaction with G protein as meta-II does, although meta-Ib exhibits a slightly lenient binding selectivity compared to that of meta-II... - Molecular properties of rhodopsin and rod functionHiroo Imai
Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606 8502, Japan
J Biol Chem 282:6677-84. 2007..Thus, the present study clearly reveals how the molecular properties of rhodopsin affect the amplitude, shape, and kinetics of the rod response... - Molecular properties of rod and cone visual pigments from purified chicken cone pigments to mouse rhodopsin in situHiroo Imai
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Photochem Photobiol Sci 4:667-74. 2005..In the present paper, we summarize the spectroscopic properties of cone pigments and describe our studies with mouse rhodopsin utilizing a high performance charge coupled device (CCD) spectrophotometer... - Physiological properties of rod photoreceptor cells in green-sensitive cone pigment knock-in miceKeisuke Sakurai
Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606 8502, Japan
J Gen Physiol 130:21-40. 2007..Therefore, the abilities of rhodopsin to generate a large single photon response and to retain high thermal stability in darkness are factors that have been necessary for the evolution of scotopic vision... - E113 is required for the efficient photoisomerization of the unprotonated chromophore in a UV-absorbing visual pigmentKei Tsutsui
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 47:10829-33. 2008..These results suggest that E113 facilitates photoisomerization in both UV-absorbing and visible light-absorbing visual pigments and provide a possible explanation for the complete conservation of E113 among vertebrate UV pigments... - Thermal recovery of iodopsin from photobleaching intermediatesYasushi Imamoto
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
Photochem Photobiol 84:941-8. 2008..As progress of the bleaching process is a consequence of protein conformational change, it is suppressed at low temperatures, resulting in thermal back-isomerization... - Photosensitivities of rhodopsin mutants with a displaced counterionKei Tsutsui
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 49:10089-97. 2010..Interestingly, all of the mutants exhibited greatly increased hydroxylamine sensitivity. This result suggests that the counterion in vertebrate visual pigments is optimally located for the stability of the Schiff base linkage... - β-arrestin functionally regulates the non-bleaching pigment parapinopsin in lamprey pinealEmi Kawano-Yamashita
Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
PLoS ONE 6:e16402. 2011..Such changes would have followed the evolution of vertebrate visual pigments, which generate unstable photoproducts that independently decay by chromophore dissociation... - Photochemical properties of mammalian melanopsinTake Matsuyama
Department of Biophysics, Graduate School of Science, Kyoto University, Japan
Biochemistry 51:5454-62. 2012..Although it is unclear whether extramelanopsin would have any physiological role, it could potentially allow wavelength-dependent regulation of melanopsin functions... - Assignment of the vibrational modes of the chromophores of iodopsin and bathoiodopsin: low-temperature fourier transform infrared spectroscopy of 13C- and 2H-labeled iodopsinsTakahiro Hirano
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
Biochemistry 45:1285-94. 2006..These results indicated that iodopsin's chromophore has a unique structure near its center and that this difference is enhanced by the binding of chloride nearby... - Multiple functions of Schiff base counterion in rhodopsinsKei Tsutsui
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606 8502, Japan
Photochem Photobiol Sci 9:1426-34. 2010..Finally, differences in the position of the counterion between vertebrate visual pigments and other opsins and its relevance to the molecular evolution of opsins are discussed... - Vertebrate ancient-long opsin has molecular properties intermediate between those of vertebrate and invertebrate visual pigmentsKeita Sato
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 50:10484-90. 2011..Thus, the molecular properties of VA/VAL opsin give insights into the mechanism of conversion of the molecular properties from invertebrate to vertebrate visual pigments... - Two-step mechanism of interaction of rhodopsin intermediates with the C-terminal region of the transducin alpha-subunitTakefumi Morizumi
Department of Biophysics, Graduate School of Science, Kyoto University, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Kyoto 606-8502
J Biochem (Tokyo) 134:259-67. 2003..These results indicate that rearrangement of the C-terminal region of Gt(alpha) after the binding of a rhodopsin intermediate is necessary for the GDP-GTP exchange reaction on Gt(alpha)... - The C-terminus of the G protein α subunit controls the affinity of nucleotidesNaoki Kimata
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 51:2768-74. 2012..Therefore, our results strongly suggest that there is a long-range interlink between the C-terminus of Giα and its nucleotide-binding site... - Depth perception from image defocus in a jumping spiderTakashi Nagata
Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
Science 335:469-71. 2012..Therefore, we propose a depth perception mechanism based on how much the retinal image is defocused... - Sexual difference in color sense in a lycaenid butterfly, Narathura japonicaMichio Imafuku
Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
Zoolog Sci 24:611-3. 2007..This male-specific UV-sensitivity is discussed in terms of ecological factors... - Opn5 is a UV-sensitive bistable pigment that couples with Gi subtype of G proteinTakahiro Yamashita
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Proc Natl Acad Sci U S A 107:22084-9. 2010..Because cOpn5m is the only UV-sensitive opsin among the opsins found so far in chicken, this study provides the molecular basis for UV reception in chicken... - First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsinTakahiro Yamashita
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
Photochem Photobiol 84:931-6. 2008..This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein... - Activation switch in the transmembrane domain of metabotropic glutamate receptorMasataka Yanagawa
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
Mol Pharmacol 76:201-7. 2009.... - Expression and localization of an exogenous G protein-coupled receptor fused with the rhodopsin C-terminal sequence in the retinal rod cells of knockin miceTakashi Kodama
Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo ku, Kyoto 606 8502, Japan
Exp Eye Res 80:859-69. 2005..In addition, a substantial fraction of the hET(B)R was successfully transported to the outer segment, suggesting that the addition of the C-terminal sequence of rhodopsin enabled hET(B)R to be translocated to the outer segment... - Bistable UV pigment in the lamprey pinealMitsumasa Koyanagi
Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology CREST, Japan Science and Technology Corporation, Kyoto 606 8502 Japan
Proc Natl Acad Sci U S A 101:6687-91. 2004..Furthermore, we isolated the parapinopsin homologues from fish and frog pineal complexes that exhibit UV sensitivity, suggesting that parapinopsin is a common molecular basis for pineal UV reception in the vertebrate... - Conserved proline residue at position 189 in cone visual pigments as a determinant of molecular properties different from rhodopsinsShigeki Kuwayama
Department of Biophysics, Graduate School of Science, Kyoto University, and Core Research for Evolutional Science and Technology (CREST, Japan Science and Technology Corporation, Kyoto 606-8502, Japan
Biochemistry 41:15245-52. 2002..The completely conserved nature of proline at position 189 could provide a clue to the molecular evolution of the pigments... - Comparative fluorescence resonance energy transfer analysis of metabotropic glutamate receptors: implications about the dimeric arrangement and rearrangement upon ligand bindingsMasataka Yanagawa
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
J Biol Chem 286:22971-81. 2011..Thus, the glutamate-dependent synergistic relocation of the helix Vs in the dimer is important for the signal flow from the extracellular ligand binding domain to the cytoplasmic surface of the mGluR... - Effect of anion binding on the thermal reverse reaction of bathoiodopsin: anion stabilizes two forms of iodopsinTakahiro Hirano
Department of Biophysics, Graduate School of Science, Kyoto University, Japan
Biochemistry 42:12700-7. 2003..Thus, iodopsin exhibits two conformational states, each of which is stabilized by the binding of chloride and nitrate, respectively... - Diversity of visual pigments from the viewpoint of G protein activation--comparison with other G protein-coupled receptorsYoshinori Shichida
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Photochem Photobiol Sci 2:1237-46. 2003.... - A novel constitutively active mutation in the second cytoplasmic loop of metabotropic glutamate receptorTakahiro Yamashita
Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology (CREST, Japan Science and Technology Corporation, Kyoto, Japan
J Neurochem 91:484-92. 2004.... - Spectroscopic analysis of the effect of chloride on the active intermediates of the primate L group cone visual pigmentTakefumi Morizumi
Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
Biochemistry 51:10017-23. 2012..These results suggest that the acquisition of H197 would be due to the most red-shifted absorption maximum, resulting in fast formation of the active state... - Amphioxus homologs of Go-coupled rhodopsin and peropsin having 11-cis- and all-trans-retinals as their chromophoresMitsumasa Koyanagi
Department of Biophysics, Graduate School of Science, Kyoto University, 606-8502, Kyoto, Japan
FEBS Lett 531:525-8. 2002..The results strongly suggest that the physiological function of peropsin would be a retinal photoisomerase, while 11-cis configuration is necessary for the Go-coupled opsin groups... - Farnesylation of retinal transducin underlies its translocation during light adaptationHidetoshi Kassai
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo 113 0033, Japan
Neuron 47:529-39. 2005....