Shigehiko Hayashi

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. ncbi request reprint Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal-mode analysis
    Shigehiko Hayashi
    Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606 8103, Japan
    J Am Chem Soc 126:10516-7. 2004
  2. pmc Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation
    Shigehiko Hayashi
    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
    Biophys J 96:403-16. 2009
  3. doi request reprint Proton-transfer reactions in reaction center of photosynthetic bacteria Rhodobacter sphaeroides
    Yu Kaneko
    Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464 8602, Japan
    J Phys Chem B 113:8993-9003. 2009
  4. doi request reprint Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single-molecule observations
    Shigehiko Hayashi
    Department of Chemistry, Graduate School of Science, Kyoto University, Japan
    J Am Chem Soc 134:8447-54. 2012
  5. ncbi request reprint [Analysis of structure and function of F1-ATPase molecular motor protein studied by molecular simulations]
    Shigehiko Hayashi
    Tanpakushitsu Kakusan Koso 52:329-34. 2007
  6. pmc Crystal structure of the channelrhodopsin light-gated cation channel
    Hideaki E Kato
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2 11 16 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Nature 482:369-74. 2012
  7. doi request reprint A theoretical study on excited state double proton transfer reaction of a 7-azaindole dimer: an ab initio potential energy surface and its empirical valence bond model
    Kohei Ando
    Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo ku, Kyoto, Japan
    Phys Chem Chem Phys 13:11118-27. 2011
  8. pmc Protein collective motions coupled to ligand migration in myoglobin
    Yasutaka Nishihara
    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto Japan
    Biophys J 98:1649-57. 2010
  9. pmc Atomistic design of microbial opsin-based blue-shifted optogenetics tools
    Hideaki E Kato
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2 11 16 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Nat Commun 6:7177. 2015
  10. pmc Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening
    Mizuki Takemoto
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    PLoS ONE 10:e0131094. 2015

Collaborators

Detail Information

Publications22

  1. ncbi request reprint Role of hydrogen-bond network in energy storage of bacteriorhodopsin's light-driven proton pump revealed by ab initio normal-mode analysis
    Shigehiko Hayashi
    Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606 8103, Japan
    J Am Chem Soc 126:10516-7. 2004
    ..Supported by agreement with observed spectra, the QM/MM calculation suggests that weakened hydrogen bonds upon photoisomerization of the chromophore are an important means of energy storage in bR...
  2. pmc Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation
    Shigehiko Hayashi
    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
    Biophys J 96:403-16. 2009
    ....
  3. doi request reprint Proton-transfer reactions in reaction center of photosynthetic bacteria Rhodobacter sphaeroides
    Yu Kaneko
    Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464 8602, Japan
    J Phys Chem B 113:8993-9003. 2009
    ....
  4. doi request reprint Molecular mechanism of ATP hydrolysis in F1-ATPase revealed by molecular simulations and single-molecule observations
    Shigehiko Hayashi
    Department of Chemistry, Graduate School of Science, Kyoto University, Japan
    J Am Chem Soc 134:8447-54. 2012
    ..The reaction mechanism unveiled here indicates that the protein can regulate the enzymatic activity for the function in both the POD and PT steps despite the fact that the RDS is the PT step...
  5. ncbi request reprint [Analysis of structure and function of F1-ATPase molecular motor protein studied by molecular simulations]
    Shigehiko Hayashi
    Tanpakushitsu Kakusan Koso 52:329-34. 2007
  6. pmc Crystal structure of the channelrhodopsin light-gated cation channel
    Hideaki E Kato
    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2 11 16 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Nature 482:369-74. 2012
    ....
  7. doi request reprint A theoretical study on excited state double proton transfer reaction of a 7-azaindole dimer: an ab initio potential energy surface and its empirical valence bond model
    Kohei Ando
    Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo ku, Kyoto, Japan
    Phys Chem Chem Phys 13:11118-27. 2011
    ..On the other hand, the computed kinetic isotope effect deviates from experimental evidence, suggesting the importance of intermolecular stretching motion, which is not explicit in the present calculations for the quantum effect...
  8. pmc Protein collective motions coupled to ligand migration in myoglobin
    Yasutaka Nishihara
    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto Japan
    Biophys J 98:1649-57. 2010
    ....
  9. pmc Atomistic design of microbial opsin-based blue-shifted optogenetics tools
    Hideaki E Kato
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2 11 16 Yayoi, Bunkyo ku, Tokyo 113 0032, Japan
    Nat Commun 6:7177. 2015
    ..The design principle we elaborate is applicable to other microbial opsins, and clarifies the underlying molecular mechanism of the blue-shifted action spectra of microbial opsins recently isolated from natural sources...
  10. pmc Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening
    Mizuki Takemoto
    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    PLoS ONE 10:e0131094. 2015
    ..These insights into the dynamics of the ground states and the early photocycle stages enhance our understanding of the channel function of ChR. ..
  11. pmc A blue-shifted light-driven proton pump for neural silencing
    Yuki Sudo
    Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464 8602, Japan
    J Biol Chem 288:20624-32. 2013
    ..Thus, we successfully produced a blue-shifted proton pump for neural silencing. ..
  12. ncbi request reprint Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method: applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution
    Masahiro Higashi
    Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo ku, Kyoto 606 8502, Japan
    J Chem Phys 126:144503. 2007
    ..They examine the nonequilibrium solvation effect on the transmission coefficient and the kinetic isotope effect for the Claisen rearrangement...
  13. doi request reprint Electronic coulombic coupling of excitation-energy transfer in xanthorhodopsin
    Kazuhiro J Fujimoto
    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606 8520, Japan
    J Am Chem Soc 131:14152-3. 2009
    ..PCI in another retinal protein, archaerhodopsin-2, which also binds a carotenoid but lacks EET activity, was also evaluated. The computed PCI is negligibly small, well explaining the lack of EET efficiency...
  14. doi request reprint Theoretical study on excited states of bacteriochlorophyll a in solutions with density functional assessment
    Masahiro Higashi
    Department of Chemistry, Biology and Marine Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903 0213, Japan
    J Phys Chem B 118:10906-18. 2014
    ....
  15. doi request reprint Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations
    Matthew J McGrath
    Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606 8502, Japan
    J Am Chem Soc 135:8908-19. 2013
    ..The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F1-ATPase, raising the possibility of a common mechanism...
  16. doi request reprint Molecular Mechanism of Wide Photoabsorption Spectral Shifts of Color Variants of Human Cellular Retinol Binding Protein II
    Cheng Cheng
    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
    J Am Chem Soc 137:13362-70. 2015
    ....
  17. doi request reprint Crucial role of protein flexibility in formation of a stable reaction transition state in an α-amylase catalysis
    Takahiro Kosugi
    Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606 8502, Japan
    J Am Chem Soc 134:7045-55. 2012
    ....
  18. doi request reprint Mechanism of efficient firefly bioluminescence via adiabatic transition state and seam of sloped conical intersection
    Lung Wa Chung
    Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606 8103, Japan
    J Am Chem Soc 130:12880-1. 2008
    ....
  19. pmc ATP hydrolysis in the betaTP and betaDP catalytic sites of F1-ATPase
    Markus Dittrich
    Beckman Institute, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Biophys J 87:2954-67. 2004
    ..The results elucidate how cooperativity between catalytic sites might be achieved by this remarkable molecular motor...
  20. pmc On the mechanism of ATP hydrolysis in F1-ATPase
    Markus Dittrich
    Beckman Institute, and Department of Physics, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Biophys J 85:2253-66. 2003
    ..Furthermore, the ATP hydrolysis reaction in beta(TP) is found to be endothermic, demonstrating that the catalytic site is able to support the synthesis of ATP and does not promote ATP hydrolysis in the particular conformation studied...
  21. pmc Thermophilic ATP synthase has a decamer c-ring: indication of noninteger 10:3 H+/ATP ratio and permissive elastic coupling
    Noriyo Mitome
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    Proc Natl Acad Sci U S A 101:12159-64. 2004
    ..This step-mismatch necessitates elastic twisting of the rotor shaft (and/or the side stalk) during rotation and permissive coupling between unit rotations by H(+) transport at F(o) and elementary events in catalysis at F(1)...
  22. pmc Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin
    Jan Saam
    Beckman Institute, University of Illinois at Urbana Champaign, 405 N Mathews Avenue, Urbana, IL 61801, USA
    Biophys J 83:3097-112. 2002
    ..This was demonstrated by a steered molecular dynamics simulation in which an applied torque enforced the rotation of helix VI...