Updated on 2023/06/07

写真a

 
Hiroto Kikuchi
 
Affiliation
Faculty of Medicine, Department of Physics, Associate Professor
Title
Associate Professor
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Research Areas

  • Nanotechnology/Materials / Fundamental physical chemistry  / 基礎物理化学関連

  • Life Science / Structural biochemistry  / 構造生物化学関連

  • Life Science / Biophysics  / bioinformatics

  • Natural Science / Biophysics, chemical physics and soft matter physics  / 生体物質の物理

  • Informatics / Computational science  / アルゴリズム

  • Life Science / Biophysics  / 数理生命科学

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Research History

  • Nippon Medical School   Medical School   Associate Professor

    2007.4

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  • Nippon Medical School   Medical School

    2004.4 - 2007.3

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  • Nippon Medical School   Medical School   Senior Assistant Professor

    1996.4 - 2004.3

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  • Nippon Medical School   Medical School

    1991.4 - 1996.3

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  • Waseda University   School of Science and Engineering

    1990.4 - 1991.3

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Committee Memberships

  • 日本物理学会   日本物理学会誌編集委員会新著紹介小委員会委員  

    1994.10 - 1996.10   

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    Committee type：Academic society

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  • 日本物理学会   生体物理分科世話人  

    1992.5 - 1993.4   

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    Committee type：Academic society

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Papers

  • Redshifting and Blueshifting of β82 Chromophores in the Phycocyanin Hexamer of Porphyridium purpureum Phycobilisomes Due to Linker Proteins Reviewed

    Hiroto Kikuchi

    Life   12 ( 11 )   1833 - 1833   2022.11

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

    Phycobilisomes in cyanobacteria and red algae are large protein complexes that absorb light and transfer energy for use in photosynthesis. The light energy absorbed by chromophores binding to phycobiliproteins in the peripheral rods can be funneled to the core through chromophores at very high efficiency. The molecular mechanism of excitation energy transfer within a phycobilisome is an example of a higher and unique function in a living organism. However, the mechanism underlying the high efficiency remains unclear. Thus, this study was carried out as a step to resolve this mechanism theoretically. The three-dimensional structure of phycobilisomes containing the linker proteins of the red alga Porphyridium purpureum was determined by cryoelectron microscopy at 2.82 Å resolution in 2020. Using these data, the absorption wavelength of each β82 chromophore in the phycocyanin hexamer located next to the core was calculated using quantum chemical treatment, considering the electric effect from its surrounding phycocyanin proteins and two linker proteins. In addition to unaffected chromophores, chromophores that were redshifted and blueshifted under the electrical influence of the two linker proteins were found. Namely, the chromophore serving as the energy sink in the rod was determined.

    DOI： 10.3390/life12111833

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  • Functional roles of the hexamer structure of C‐phycocyanin revealed by calculation of absorption wavelength Reviewed

    Hiroto Kikuchi

    FEBS Open Bio   10 ( 11 )   1 - 9   2020.11

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

    File： FEBS_Open_Bio_10(11)_2020-11-29.pdf

    DOI： 10.1002/2211-5463.13038

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    Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/2211-5463.13038

  • 汎用性ある分子振動のB行列作成方法と力定数の座標変換方法に関する考察

    菊地浩人

    日本医科大学基礎科学紀要   ( 42 )   37 - 85   2013.9

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    Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：日本医科大学  

    File： 日本医科大学基礎科学紀要　第42号 37~84頁，(2013年).pdf

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  • Different inhibitory potency of febuxostat towards mammalian and bacterial xanthine oxidoreductases: insight from molecular dynamics Reviewed

    Hiroto Kikuchi, Hiroshi Fujisaki, Tadaomi Furuta, Ken Okamoto, Silke Leimkuehler, Takeshi Nishino

    SCIENTIFIC REPORTS   2   srep00331-1 - srep00331-8   2012.3

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：NATURE PUBLISHING GROUP  

    Febuxostat, a drug recently approved in the US, European Union and Japan for treatment of gout, inhibits xanthine oxidoreductase (XOR)-mediated generation of uric acid during purine catabolism. It inhibits bovine milk XOR with a K-i in the picomolar-order, but we found that it is a much weaker inhibitor of Rhodobacter capsulatus XOR, even though the substrate-binding pockets of mammalian and bacterial XOR are well-conserved as regards to catalytically important residues and three-dimensional structure, and both permit the inhibitor to be accommodated in the active site, as indicated by computational docking studies. To clarify the reason for the difference of inhibitory potency towards the two XORs, we performed molecular dynamics simulations. The results indicate that differences in mobility of hydrophobic residues that do not directly interact with the substrate account for the difference in inhibitory potency.

    File： Sci. Rep. (Nature.com) 2 Article number 331, (2012).pdf

    DOI： 10.1038/srep00331

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  • Combined Biophysical and Biochemical Study of Enzyme Effects: Binding Mechanism of an Inhibitor Febuxostat with Xanthine Oxidoreductase Reviewed

    Fujisaki Hiroshi, Furuta Tadaomi, Okamoto Ken, Kikuchi Hiroto

    Nihon Ika Daigaku Igakkai Zasshi   8 ( 3 )   222 - 227   2012

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    Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：The Medical Association of Nippon Medical School  

    We review our recent collaborative study, performed by computational physicists and biochemists, of the enzyme effects due to the drug called febuxostat. Febuxostat, which was recently approved in the US, European Union and Japan for treatment of gout, inhibits xanthine oxidoreductase (XOR)-mediated generation of uric acid during purine catabolism. Experiments have shown that febuxostat has strong effects on mammalian XOR but not on bacterial XOR, although the two enzymes have similar three-dimensional structures. To clarify the difference in the inhibitory power of febuxostat, we performed docking and molecular dynamics simulations for mammalian and bacterial XORs. We found that the static structures are not sufficient to explain the binding difference and that important interactions occur between febuxostat and the active region of the enzymes which suggests a better strategy for drug design.<br>

    File： 日医大医会誌，第8巻　第3号，222~227頁，(2012年).pdf

    DOI： 10.1272/manms.8.222

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    Other Link： http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100641427

  • 溶媒中にある励起分子からの一光子発光に対する理論的アプローチ―基本方程式の導出― Reviewed

    梅崎馨章, 菊地浩人, 小田井圭

    Proc Sch Sci Tokai Univ   43   107 - 125   2008.3

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    Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：東海大学  

    We have derived a line-shape function [J. Chem. Phys. 124, 074304 (2006); Proc. Sch. Sci, Tokai Univ. 41, 83 (2006)] for the spontaneous emission from an electronically excited molecule in a solvent on the basis of following assumptions: (i) The initial state of an excited molecule is thermalized; (ii) the interaction between the excited molecule and a solvent can be disregarded during the time evolution of the system under consideration. In this paper, excluding the latter assumption (ii), we develop the time evolution of an excited molecule in a solvent using a reduced density operator, and derive a basic equation for calculating a transition rate. As an example, we show that its basic equation leads to a line-shape function on the assumptions (i) and (ii) in the weak limiting case of the interaction between an excited molecule and a solvent.

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  • Molecular analysis of TCR and peptide/MHC interaction using P18-I10-derived peptides with a single D-amino acid substitution Reviewed

    Yohko Nakagawa, Hiroto Kikuchi, Hidemi Takahashi

    BIOPHYSICAL JOURNAL   92 ( 7 )   2570 - 2582   2007.4

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：BIOPHYSICAL SOCIETY  

    For the structural analysis of T-cell receptor (TCR) and peptide/MHC interaction, a series of peptides with a single amino acid substitution by a corresponding D-amino acid, having the same weight, size, and charge, within P18-I10 (aa318-327: RGPGRAFVTI), an immunodominant epitope of HIV-1 IIIB envelope glycoprotein, restricted by the H-2D(d) class I MHC molecule, has been synthesized. Using those peptides, we have observed that the replacement at positions 324F, 325V, 326T, and 327I with each corresponding D-amino acid induced marked reduction of the potency to sensitize targets for P18-I10specific murine CD8(+) cytotoxic T lymphocytes (CTLs), LINE-IIIB, recognition. To analyze further the role of amino acid at position 325, the most critical site for determining epitope specificity, we have developed a CTL line [LINE-IIIB(325D)] and its offspring clones specific for the epitope I-10(325v) having a D-valine (v) at position 325. Taking advantage of two distinct sets of CD8(+) CTLs restricted by the same D-d, three-dimensional structural analysis on TCR and peptide/MHC complexes by molecular modeling was performed, which indicates that the critical amino acids within the TCRs for interacting with 325V or 325v appear to belong to the complementarity- determining region 1 but not to the complementarity- determining region 3 of V ss chain.

    File： Biophys. J. 92, 2570-2582, (2007).pdf

    DOI： 10.1529/biophysj.106.095208

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  • スペクトル形状関数の定式化‐分子の構造変化及び力定数の変化による表現― Reviewed

    梅崎馨章, 菊地浩人

    Proc Sch Sci Tokai Univ   41   83 - 104   2006.3

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    Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)   Publisher：東海大学  

    Normal mode coordinates of one electronic state are generally different from those of other electronic state. This difference causes mathematical complexity for describing line shape functions (LSFs) associated with transition between initial and final electronic states, so that only the effect of change in molecular structure in the transition has often been considered in LSF. However, the effect of change in force constants is another significant factor for LSF. In the present paper, using not generating function method but rather the density matrix method, we derive a new expression of LSF including the effects of change in force constants as well as the effect of change in molecular structure within harmonic oscillator approximation.

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  • A line-shape function in terms of changes in both molecular structure and force constants: A Gaussian approximation Reviewed

    K Umesaki, H Kikuchi

    JOURNAL OF CHEMICAL PHYSICS   124 ( 7 )   074304-1 - 074304-11   2006.2

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    Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

    We propose a new expression of a line-shape function (LSF) including the effects of changes in both force constants and the molecular structure within the harmonic-oscillator approximation. This expression enables us to calculate the LSF using only the data on molecular structures, force constants, and electronic energies in the initial and final electronic states without solving the eigenvalue equation for the normal vibration of a molecule. To derive the LSF expression, we consider one-photon emission from a polyatomic molecule thermalized in an electronic excited state, and derive the intensity distribution function for one-photon emission using not Lax and Kubo and Toyozawa's [J. Chem. Phys. 20, 1752 (1952); Prog. Theor. Phys. 13, 160 (1955)] generating function method but rather the density-matrix method. As a simple application, a Gaussian approximate LSF is applied to SO2. As a result, it is found that the effect of change in force constants between the initial and final electronic states cannot be ignored, nor can the effect of change in the molecular structure between these two states. The LSF expression obtained is applicable to studies of not only radiative transition but also of electron-transfer and energy-transfer processes where both changes in molecular structure and force constants between the initial and final electronic states cannot be disregarded.

    File： J. Chem. Phys. 124, 074304-1-11, (2006).pdf

    DOI： 10.1063/1.2166630

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  • Computational method for calculating multidimensional Franck-Condon factors: Based on Sharp-Rosenstock's method Reviewed

    H Kikuchi, M Kubo, N Watanabe, H Suzuki

    JOURNAL OF CHEMICAL PHYSICS   119 ( 2 )   729 - 736   2003.7

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

    Normal mode coordinates of vibrational states associated with one electronic state are generally different from those of vibrational states associated with other electronic states in polyatomic molecules (normal coordinate mixing). This has prevented the multidimensional Franck-Condon integrals from being widely used in spite of their importance. We introduce a simple, noncumbersome numerical computer method for calculating those integrals despite including a mixing of the normal coordinates in the harmonic oscillator approximation on the basis of the expressions by Sharp and Rosenstock. We also introduce more simple expressions of Sharp-Rosenstock's formulas. (C) 2003 American Institute of Physics.

    File： J. Chem. Phys. 119, 729-736, (2003).pdf

    DOI： 10.1063/1.1571522

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  • Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis Reviewed

    H Kikuchi, H Wako, K Yura, M Go, M Mimuro

    BIOPHYSICAL JOURNAL   79 ( 3 )   1587 - 1600   2000.9

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：BIOPHYSICAL SOCIETY  

    Phycobiliproteins are basic building blocks of phycobilisomes, a supra-molecular assembly for the light-capturing function of photosynthesis in cyanobacteria and red algae. One functional form of phycobiliproteins is a trimeric form consisting of three identical units having C-3 symmetry, with each unit composed of two kinds of subunits, the alpha-subunit and beta-subunit. These subunits have similar chain folds and can be divided into either globin-like or X-Y helices domains. We studied the significance of this two-domain structure for their assembled structures and biological function (light-absorption) using a normal mode analysis to investigate dynamic aspects of their three-dimensional structures. We used C-phycocyanin (C-PC) as an example, and focused on the interactions between the two domains. The normal mode analysis was carried out for the following two cases: 1) the whole subunit, including the two domains; and 2) the globin-like domain alone. By comparing the dynamic properties, such as correlative movements between residues and the fluctuations of individual residues, we found that the X-Y helices domain plays an important role not only in the C-3 symmetry assemblies of the subunits in phycobiliproteins, but also in stabilizing the light absorption property by suppressing the fluctuation of the specific Asp residues near the chromophore. Interestingly, the conformation of the X-Y helices domain corresponds to that of a module in pyruvate phosphate dikinase (PPDK). The module in PPDK is involved in the interactions of two domains, just as the X-Y helices domain is involved in the interactions of two subunits. Finally, we discuss the mechanical construction of the C-PC subunits based on the normal mode analysis.

    File： Biophys. J. 79, 1587-1600, (2000).pdf

    DOI： 10.1016/S0006-3495(00)76409-5

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  • A Theoretical Study of the Mechanism of Excitation Energy Transfer between Biomolecules : An Investigation of Forster's Formula and Its Expansion Reviewed

    UMEZAKI Keisho, KIKUCHI Hiroto

    The bulletin of liberal arts & sciences, Nippon Medical School   28   1 - 21   2000.6

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    Authorship：Corresponding author   Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)   Publisher：日本医科大学  

    File： 日本医科大学基礎科学紀要 第28号, 1～21頁，(2000年).pdf

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  • Phycobilisomes: Supramolecular Assembly in Cyanobacteria for Capturing of Light Energy.

    三室守, 村上明男, 菊地浩人

    蛋白質 核酸 酵素   42 ( 16 )   2613 - 2625   1997.12

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    Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：共立出版  

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  • An electronic state of the chromophore, phycocyanobilin, and its interaction with the protein moiety in C-phycocyanin: protonation of the chromophore Reviewed

    H Kikuchi, T Sugimoto, M Mimuro

    CHEMICAL PHYSICS LETTERS   274 ( 5-6 )   460 - 465   1997.8

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

    An electronic state of phycocyanobilin (PCB, a derivative of an open tetrapyrrole) in C-phycocyanin, an antenna pigment-protein complex for photosynthesis, was estimated by including the effect of an electrostatic field of protein moieties and water molecules. We adapted our unique method for calculation of the resonance integral. The observed absorption wavelength and an oscillator strength were reproduced only when the PCB was assigned to the protonated form with a net charge of 1. This was rationalized by the negative charge of a specific aspartate residue which was equidistant from the two nitrogen atoms of two central pyrrole rings. (C) 1997 Elsevier Science B.V.

    File： Chem. Phys. Lett. 274, 460-465, (1997).pdf

    DOI： 10.1016/S0009-2614(97)00659-3

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  • Dynamical theory of photoisomerization of the rhodopsin chromophore: Generation of a transient electric field during photoisomerization Reviewed

    H Kikuchi, H Suzuki

    JOURNAL OF PHYSICAL CHEMISTRY B   101 ( 31 )   6050 - 6056   1997.7

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

    Photoisomerization of the rhodopsin chromophore is one of the typical nonadiabatic transitions. We have proposed a new dynamical theory of photoisomerization of the chromophore based on quantum mechanics. We have considered the transient excited state DES (deformed excited state: Psi(D)) of electrons, which has different lengths for stabilization from those in the excited state immediately after the absorption of light, together with the lowest electronic state VGS (virtual ground state: Psi(V)), which has the same bond lengths as Psi(D). We have also considered the normal vibrational states {U-rj(Theta)} associated with these transient electronic states {Psi(r)(Theta)} (Theta represents the angle of cis-trans isomerization). With these preliminary assumptions, the nonstationary state Phi(t) of the chromophore has been expressed as an expansion in {Psi(r)(Theta)U-rj(Theta)}, and the time-dependent equation for its coefficients {b(rj)(t)} has been derived rigorously by explicitly taking into account the kinetic energy of atomic cores. On these bases, in the present study we calculate a transient electric field caused by the change of the net charges in the chromophore during photoisomerization. To examine the effect of this field on the protein moiety around the chromophore, we calculate by way of example the interaction between formamide and a constant electric field. The results demonstrate that the net charges in formamide are considerably affected by the constant electric field. We then apply this calculation to a bacteriorhodopsin model and also demonstrate the change of the net charges in the amino acids near the chromophore. Finally, we point out that the change of the net charges in the amino acids and the vibrational-vibrational interaction between the chromophore and its surrounding opsin are crucial.

    File： J. Phys. Chem. B. 101, 6050-6056, (1997).pdf

    DOI： 10.1021/jp962015i

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  • DYNAMICAL THEORY OF THE PHOTOISOMERIZATION OF RHODOPSIN CHROMOPHORE .2. HOW TO CALCULATE THE INTEGRALS RELATED WITH TRANSIENT PI-ELECTRONIC STATES Reviewed

    H KIKUCHI, K ODAI, H SUZUKI

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   64 ( 3 )   1011 - 1022   1995.3

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：PHYSICAL SOC JAPAN  

    Based on the ZDO approximation of the LCAO-ASMO-SCF-CI theory of pi-electrons, we show the methods of calculating the integrals [Psi(r)\partial derivative Psi(s)/partial derivative Theta], [Psi(r)\del(d)(T)G del(d)Psi(s)] and [Psi(r)\Delta(d)(T) Psi(s)] in the basic equation of photoisomerization which was derived in the pervious paper I with a due account of the kinetic energy of atomic cores. Here {Psi(r)} represent the transient pi-electronic states of rhodopsin chromophore; Theta does the angle of photoisomerization; d is the internal displacement coordinate of the chromophore; G denotes the matrix G in Wilson's GF matrix method. It is also shown that the second and third integrals mentioned above can be reduced to the first one in a good approximation, and that the three integrals play very important roles in the photoisomerization of the chromophore.

    File： J. Phys. Soc. Jpn. 64, 1011-1022, (1995).pdf

    DOI： 10.1143/JPSJ.64.1011

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  • Dynamical theory of the photoisomerization of rhodopsin Chromophore. I: Calculations of the transition probability Reviewed

    H. Kikuchi, H. Suzuki

    J. Phys. Soc. Jpn.   61 ( 6 )   1946 - 1959   1992

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：The Physical Society of Japan (JPS)  

    Assuming that the stretching-vibrational energy of rhodopsin chromophore dissipates to the protein moiety during the photoisomerization, we consider the deformed excited state Ψ 2 and the virtual ground state Ψ 1 of the π-electron system. We also consider the normal vibrational states { U r j } of the stretching and torsional vibrations in these transient π-electronic states {Ψ r }. The non-stationary state of the chromophore is then expressed as a linear combination of {Ψ r U r j }, and the equation for its coefficients is derived by explicitly taking account of the kinetic energy of atomic cores. On this basis, the probability of the non-adiabatic transition from Ψ 2 to Ψ 1 is calculated as a function of the angle of cis-trans isomerization, as well as the energy dissipation from the chromophore to confirm the reasonability of our proposition of {Ψ r }.

    File： J. Phys. Soc. Jpn. 61, 1946-1959, (1992).pdf

    DOI： 10.1143/JPSJ.61.1946

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  • A Method to Calculate Functions of the Product of G and F used in Wilson’s GF Matrix method Reviewed

    H.Kikuchi

    IJTSRD   2 ( 4 )   2516 - 2519   2018.6

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    Language：English   Publishing type：Research paper (scientific journal)  

    File： ijtsrd15667(2018-6).pdf

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  • キサンチン酸化還元酵素―物理学から臨床医学まで― Reviewed

    岡本 研, 菊地浩人

    日本医科大学基礎科学紀要   46 ( 46 )   37 - 69   2018

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    Language：Japanese   Publishing type：Research paper (scientific journal)  

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  • Vibrational energy transport in acetylbenzonitrile described by an ab initio-based quantum tier model Reviewed

    Hiroshi Fujisaki, Kiyoshi Yagi, Hiroto Kikuchi, Toshiya Takami, Gerhard Stock

    CHEMICAL PHYSICS   482   86 - 92   2017.1

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

    Performing comprehensive quantum-chemical calculations, a vibrational Hamiltonian of acetylbenzonitrile is constructed, on the basis of which a quantum-mechanical "tier model" is developed that describes the vibrational dynamics following excitation of the CN stretch mode. Taking into account 36 vibrational modes and cubic and quartic anharmonic couplings between up to three different modes, the tier model calculations are shown to qualitatively reproduce the main findings of the experiments of Rubtsov and coworkers (2011), including the energy relaxation of the initially excited CN mode and the structure dependent vibrational transport. Moreover, the calculations suggest that the experimentally measured cross-peak among the CN and CO modes does not correspond to direct excitation of the CO normal mode but rather reflects excited low-frequency vibrations that anharmonically couple to the CO mode. Complementary quasiclassical trajectory calculations are found to be in good overall agreement with the quantum calculations. (C) 2016 Elsevier B.V. All rights reserved.

    File： Chem. Phys.(2017)Fujisakli.pdf

    DOI： 10.1016/j.chemphys.2016.09.010

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  • 3P047 Mutation studies on the mammalian and the baterial XORs with inhibitors(01A. Protein: Structure,Poster)

    Kikuchi Hiroto, Fujisaki Hiroshi, Furuta Tadaomi, Okamoto Ken, Nishino Takeshi

    Seibutsu Butsuri   53 ( 1 )   S219   2013

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.53.S219_5

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  • 2PT137 Molecular dynamics simulations and binding free energy analysis of xanthine oxidoreductase-ligand complexes(The 50th Annual Meeting of the Biophysical Society of Japan)

    Kikuchi Hiroto, Fujisaki Hiroshi, Furuta Tadaomi, Okamoto Ken, Nishino Takeshi

    Seibutsu Butsuri   52   S128   2012

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.52.S128_3

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  • Molecular Orbital Study of the Interaction between MgATP and the Myosin Motor Domain Using the PM6 Reviewed

    H. Kagawa, H. Kikuchi, Q. Gao, T. Ogihara

    J. Comp. Chem. Jpn.   9 ( 1 )   37 - 42   2010

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Society of Computer Chemistry, Japan  

    Previously, our research group carried out molecular orbital studies of the interaction between MgATP and the myosin motor domain using the PM3 method of MOPAC97. In this study, we present recalculation results obtained using the PM6 method of MOPAC2009 and discuss the problems that may be encountered in further studies. Previous research carried out by our group in this field is introduced briefly. Furthermore, it is proposed that the increase in the distance between Pγ and the bridging O atom bound to Pβ initiates the dissociation of γ-phosphate from ATP. Our results demonstrate that semi-empirical molecular orbital methods are useful in studying the chemical reactions underlying the initial step of ATP hydrolysis in the myosin motor domain.

    File： J. Comp. Chem. 9(1), 37-42, (2010).pdf

    DOI： 10.2477/jccj.H2127M

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  • 3P031 Molecular dynamics study of the interaction between xanthine oxidoreductase and the inhibitor(Protein: Structure & Function,The 48th Annual Meeting of the Biophysical Society of Japan)

    Kikuchi Hiroto, Fujisaki Hiroshi, Furuta Tadaomi, Okamoto Ken, Leimkuhler Silke, Nishino Takeshi

    Seibutsu Butsuri   50 ( 2 )   S150   2010

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.50.S150_3

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  • 2P161 Molecular Orbital Analysis to investigate the Reaction Mechanism of ATP Hydrolysis in Myosin Motor Domain(The 48th Annual Meeting of the Biophysical Society of Japan)

    Kagawa Hiroshi, Kikuchi Hiroto, Fujisaki Hiroshi, Nagai Yoshinori, Wako Hiroshi

    Seibutsu Butsuri   50 ( 2 )   S110 - S111   2010

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.50.S110_5

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  • 3P-023 Significance of enzyme fluctuation in the lock-key mechanism between xanthine oxidoreductase and Febuxostat(Protein:Structure & Function,The 47th Annual Meeting of the Biophysical Society of Japan)

    Kikuchi Hiroto, Fujisaki Hiroshi, Furuta Tadaomi, Okamoto Ken, Nishino Takeshi, Leimkuhler Silke

    Seibutsu Butsuri   49   S154   2009

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.49.S154_5

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  • 1P-053 Molecular dynamics study of xanthine oxidoreductases (XOR) : interaction between XOR and its inhibitor(The 46th Annual Meeting of the Biophysical Society of Japan)

    Kikuchi Hiroto, Fujisaki Hiroshi, Okamoto Ken, Leimkuhler Silke, Nishino Takeshi

    Seibutsu Butsuri   48   S29   2008

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.48.S29_1

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  • 2P142 Dynamic structure of xanthine oxidoreductase by normal mode analysis(33. Redox enzyme,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

    Kikuchi Hiroto, Watanabe Noboru, Okamoto Ken, Leimkuler Silke, Nishino Takeshi

    Seibutsu Butsuri   46 ( 2 )   S331   2006

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    Language：English   Publisher：The Biophysical Society of Japan General Incorporated Association  

    DOI： 10.2142/biophys.46.S331_2

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  • Theory of Transition Rates of Excitation Energy Transfer between Weak Interacting Molecules in a Radiation Field : Formulation Based on a Dipole Approximation Reviewed

    UMEZAKI Keisho, KIKUCHI Hiroto

    The bulletin of liberal arts & sciences, Nippon Medical School   29   9 - 27   2000.12

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    Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)   Publisher：日本医科大学  

    CiNii Books

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  • Simple fluctuation of Ca2+ elicits the complex circadian dynamics of cyclic AMP and cyclic GMP in Paramecium Reviewed

    K. Hasegawa, H. Kikuchi, S. Ishizaki, A. Tamura, Y. Nakaoka, E. Iwai, T. Sato

    J. Cell. Sci.   112 ( 2 )   201 - 207   1999.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    File： J. Cell. Sci. 112, 201-207, (1999).pdf

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  • An Approximate Expression of Expectation Values for Energy by INDO-CI Method

    K. Umesaki, H. Kikuchi

    Mem. Kokushi-kan Univ. CIS.   17 ( 17 )   20 - 35   1996.3

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    Language：English   Publishing type：Research paper (bulletin of university, research institution)   Publisher：国士館大学情報科学センタ-  

    File： Mem. Kokushi-kan Univ. CIS. 17, 20-35, (1996).pdf

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  • 視物質発色団の光異性化に対する動力学的理論(II)―過渡的電子状態に関連した諸積分の計算方法― Reviewed

    H. Suzuki, H. Kikuchi, T. Shimabukuro

    Bulletin of Science and Engineering Research Laboratory   ( 142 )   79 - 89   1993.6

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    Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)  

    File： 早稲田大学理工学研究所報告 第142輯，79～89頁，(1993年).pdf

    CiNii Books

    J-GLOBAL

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  • LCAO-ASMO-SCF-CI法およびそのZDO近似による励起π電子状態のエネルギ-期待値 Reviewed

    菊地 浩人, 梅崎 馨章, 鈴木 英雄

    早稲田大学理工学研究所報告   ( 127 )   58 - 67   1990

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    Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)   Publisher：早稲田大学理工学研究所  

    File： 6_早稲田大学理工学研究所報告 第127輯，58～67頁，(1990年).pdf

    CiNii Books

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  • Dynamical theory of the photoisomerization of visual-pigment chromophore. (I). Derivation of the basic equation. Reviewed

    鈴木英雄, 菊地浩人, 梅崎馨章

    早稲田大学理工学研究所報告   ( 126 )   84 - 92   1989.11

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    Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)  

    File： 7_早稲田大学理工学研究所報告 第126輯，84～92頁，(2000年).pdf

    CiNii Books

    J-GLOBAL

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  • Stretching-torsional vibration modes in the excited states of rhodopsin chromophore.

    菊地浩人, 伊藤悦朗, 鈴木英雄

    早稲田大学理工学研究所報告   ( 122 )   71 - 82   1989.1

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    Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)   Publisher：早稲田大学理工学研究所  

    File： 8_早稲田大学理工学研究所報告 第122輯，71～82頁，(1989年).pdf

    CiNii Books

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  • SEMIEMPIRICAL CALCULATIONS OF FORCE-CONSTANTS FOR TORSIONAL AND STRETCHING VIBRATIONS IN EXCITED-STATES OF RETINAL AND ITS RELATED-COMPOUNDS Reviewed

    E ITO, H KIKUCHI, H SUZUKI

    JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN   57 ( 5 )   1842 - 1851   1988.5

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：PHYSICAL SOCIETY JAPAN  

    We consider the ground state (GS), the excited state on absorption (ESA), the virtual ground (VGS) and the deformed excited state (DES) of π-electron system in hexaene, retinal, retinal Schiff-base (RSB), protonated retinal Schiff-base (PRSB) or our model for rhodopsin chromophore, and we semiempirically calculate the following two kinds of force constants for the pairs of bonded atoms in each of the four π-electronic states: (1) the force constants of torsional vibrations; (2) those of the interactions between torsional and stretching vibrations. The calculations are carried out by our LCAO-ASMO-SCF-CI method for π-electrons, selecting such a part of the total energy of π-electron system that gives a significant contribution to the force constants.

    File： 13_J. Phys. Soc. Jpn. 57, 1842-1851, (1988).pdf

    DOI： 10.1143/JPSJ.57.1842

    Web of Science

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Books

  • Antenna systems and energy transfer in cyanophyta and rhodophyta. In: Light-harvesting Antennas in Photosynthesis edited by B. R. Green and W. W. Parson. Advanced in Photosynthesis and Respiration: Series Editor Govindjee

    M. Mimuro, H. Kikuchi（ Role： Contributorpp. 281-306）

    Springer, The Netherlands  2003  （ ISBN:9780792363354 ）

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    Responsible for pages：pp. 281-306   Language：English   Book type：Scholarly book

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  • Structure and Function of Phycobilisome. In: Concepts in Photobiology: Photosynthesis and Photomorphogenesis edited by G. S. Singhal, G. Renger, S.K. Sopory, K-D. Irrgang and Govindjee

    Mamoru MIMURO, Hiroto KIKUCHI, Akio MURAKAMI（ Role： Contributorpp. 104-135）

    Springer, The Netherlands  1999  （ ISBN:9789401148320 ）

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    Responsible for pages：pp. 104-135   Language：English   Book type：Scholarly book

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  • Functional meaning of the symmetry structure in phycobiliprotein aggregates. In: Proceeding of XIth International Congress on Photosynthesis: Mechanisms and Effects

    H. Kikuchi, H. Wako, M. Go, M. Mimuro（ Role： Contributorpp. 193-196）

    Springer, The Netherlands  1998 

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  • Circadian cellular spatiotemporal organization conducted by simple Ca2+ oscillation, Neuroscience Research, Vol. 31, Suppl. 1

    K. Hasegawa, H. Kikuchi, S. Ishizaki, Y. Tsukahara, E. Iwai（P. S212）

    ELSEVIER, The Netherlands  1998 

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  • Rigid domain in static and dynamic structures of proteins, Progress in Biophysics and Molecular Biology, Vol. 65, Suppl. 1

    H. Wako, H. Kikuchi（P. 36）

    ELSEVIER, The Netherlands  1996 

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Misc.

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Research Projects

  • 基盤研究（Ｃ）[研究代表者]「ヒトには効くがバクテリアには効かない痛風薬 ―酵素薬剤相互作用のダイナミクス―」

    2014.4 - 2017.3

    文科省  科学研究費補助金 

    菊地 浩人

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    Authorship：Principal investigator  Grant type：Competitive

    Grant amount：\4940 （ Direct Cost: \3800 、 Indirect Cost：\1140 ）

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  • 基盤研究（Ｃ）[研究代表者]「キサンチン酸化還元酵素における阻害剤の研究 ―「鍵と鍵穴」のドグマを超えて―」

    2011.4 - 2013.3

    文科省  科学研究費補助金 

    菊地 浩人

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    Authorship：Principal investigator  Grant type：Competitive

    Grant amount：\4810 （ Direct Cost: \3700 、 Indirect Cost：\1110 ）

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  • 基盤研究（Ｃ）[研究分担者]「生体分子の量子ダイナミクス:その理論的解明と制御」

    2010.4 - 2013.3

    文科省  科学研究費補助金 

    藤崎 弘士

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    Grant type：Competitive

    Grant amount：\2860 （ Direct Cost: \2200 、 Indirect Cost：\660 ）

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  • 基盤研究（Ａ） [研究分担者] 「モリブデン金属酵素の微細構造と水酸化反応機構・蛋白質揺らぎの解明」

    2004.4 - 2008.3

    文科省  科学研究費補助金 

    西野 武士

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    Grant type：Competitive

    Grant amount：\48230 （ Direct Cost: \37100 、 Indirect Cost：\11130 ）

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  • 萌芽的研究 [研究分担者] 「基準振動解析による蛋白質の構造の必然性の解明―光合成系を例にして」

    1999.4 - 2001.3

    文部省  科学研究費補助金 

    三室 守

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    Grant type：Competitive

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  • 基盤研究（Ａ）[研究分担者]「蛋白質集合体の対称性の起源と系譜－機能的要請か、系統性か」

    1996.4 - 1998.3

    文部省  科学研究費補助金 

    三室 守

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    Grant type：Competitive

    Grant amount：\11200 （ Direct Cost: \11200 ）

    光合成、視覚などのエネルギー変換、情報変換過程で機能する蛋白質集合体でしばしば観察される蛋白質分子の対称構造の意味を、(1)機能発現のための必然性、(2)起源が異なる蛋白質の系統性、のふたつの観点から考察した。具体的な解析のポイントは、(1)補欠分子間の相互作用、(2)ドメイン、さらにモデュール構造であった。解析の対象として、光合成系反応中心(C_2対称)、アンテナ複合体(C_3対称)、ロドプシンファミリー(C_3対称、対称性は不変)、対称性と同じ意味で重要な「対称性の破れと機能発現」の観点から、ATPase(偽C_3対称、対称性は不変)を考察した。
    光合成アンテナ系の場合、対称構造を取ることは最も容易に光を集める効率を高めることが可能な方法である。しかしこれを機能発現の「必然性」として理解できる例は多くはない。例えば、フィコビリン蛋白質はグロビン蛋白質のN末端側にヘリックス構造を加えて、グロビン蛋白質とは異なる対称性を確保し、同時に機能発現のために色素間での相互作用を可能にしたケースである。この場合、基準振動解析から構造的な必然性を証明することができた。
    ATPaseは,機能の発現のためにその対称性を破ることが必然であることが最近明らかになった3次元構造からも理解された。
    班会議での結論は、この課題は今後,蛋白質の3次元構造が集積する中で、機能と密接に結び付いた課題であり、長期的な展望に立って継続する必要があることが確認された。

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