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2013 Fiscal Year Final Research Report

Quantum chemical studies on a cooperative proton and electron transfer reaction in protein

Research Project

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Project/Area Number 22685003
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Physical chemistry
Research InstitutionOsaka University (2011-2013)
University of Hyogo (2010)

Principal Investigator

SHIGETA Yasuteru  大阪大学, 基礎工学研究科, 准教授 (80376483)

Project Period (FY) 2010-04-01 – 2014-03-31
Keywords量子動力学 / 電子移動 / 水素移動 / 集団運動 / PCET
Research Abstract

In this project, we have investigated a proton pumping mechanism of a cytochrom c oxidase, which is a fundamental enzyme for the biological energy transduction, on the basis of quantum mechanics. In particular, we have analyzed the energetics and dynamics of protons in D-pathway, which is one of proton pumping pathways, and found that (1) energy barrier for the pumped proton becomes less due to protein environment in comparison with gas phase environment (2) a rotation of His residue at the D-pathway prevent the backward flow of the proton.

  • Research Products

    (48 results)

All 2014 2013 2012 2011 2010 Other

All Journal Article (30 results) Presentation (16 results) Book (2 results)

  • [Journal Article] On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase2014

    • Author(s)
      T. Baba, R. Harada, M. Nakano, Y. Shigeta
    • Journal Title

      J. Comp. Chem

      Volume: 35 Pages: 1240-1247

  • [Journal Article] Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins2014

    • Author(s)
      R. Harada, Y. Takano, Y. Shigeta
    • Journal Title

      J. Chem. Phys

      Volume: 140 Pages: 125103

  • [Journal Article] A Nylon-oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds2014

    • Author(s)
      K. Kamiya, T. Baba, M. Boero, T. Matsui, S. Negoro, Y. Shigeta
    • Journal Title

      J. Phys. Chem. Lett

      Volume: 5 Pages: 1210-1216

  • [Journal Article] 第一原理Meta-Dynamics 法, Blue Moon Ensemble法を用いた反応経路解析 (特集 反応経路探索)2014

    • Author(s)
      馬場剛史, 安東寛之, 重田 育照
    • Journal Title

      アンサンブル : 分子シミュレーション研究会会誌

      Volume: 16, Vol.1 Pages: 36-41

  • [Journal Article] Cumulant mechanics : An explicit treatment for fluctuation on dynamics2013

    • Author(s)
      Y. Shigeta
    • Journal Title

      分子科学会アーカイブス(Review), Mol. Sci

      Volume: 7, Vol.1 Pages: A0057

  • [Journal Article] 第一原理計算による生体内酵素反応の理論解析2013

    • Author(s)
      重田育照
    • Journal Title

      豊田研究報告

      Volume: 66 Pages: 103-104

  • [Journal Article] Theoretical studies of electronic structures, magnetic properties and electron conductivities of one-dimensional Ni_n (n = 3, 5, 7) complexes2013

    • Author(s)
      Y. Kitagawa, T. Matsui, Y. Nakanishi, Y. Shigeta, T. Kawakami, M. Okumura, K. Yamaguchi
    • Journal Title

      Dalton Trans

      Volume: 42 Pages: 16200-16208

  • [Journal Article] Binding of a positron to nucleic-acid base molecules and their pairs2013

    • Author(s)
      K. Koyanagi, Y. Kita, Y. Shigeta, M. Tachikawa
    • Journal Title

      ChemPhysChem

      Volume: 14 Pages: 3458-3462

  • [Journal Article] Finite-Field Method with Unbiased Polarizable Continuum Model for Evaluation of the Second Hyperpolarizability of an Open-Shell Singlet Molecule in Solvents2013

    • Author(s)
      T. Inui, Y. Shigeta, K. Okuno, T. Baba, R. Kishi, M. Nakano
    • Journal Title

      J. Comp. Chem

      Volume: 34 Pages: 2345-2352

  • [Journal Article] Non-empirical tuning of CAM-B3LYP functional in time-dependent density functional theory for excitation energies of diarylethene derivatives2013

    • Author(s)
      K. Okuno, Y. Shigeta, R. Kishi, M. Nakano
    • Journal Title

      Chem. Phys. Lett

      Volume: 585 Pages: 201-206

  • [Journal Article] Photochromic Switching of Diradical Character : Design of Efficient Nonlinear Optical Switches2013

    • Author(s)
      K. Okuno, Y. Shigeta, R. Kishi, M. Nakano
    • Journal Title

      J. Phys. Chem. Lett

      Volume: 4 Pages: 2418-2422

  • [Journal Article] A Density Functional Theory Based Protocol to Compute the Redox Potential of Transition Metal Complex with the Correction of Pseudo-Counterion : General Theory and Applications2013

    • Author(s)
      T. Matsui, Y. Kitagawa, Y. Shigeta, M. Okumura
    • Journal Title

      J. Chem. Theor. Comp

      Volume: 9 Pages: 2974-2980

  • [Journal Article] Qantal Cumulant Mechanics and Dynamics for Multi-Dimensional Quantum Many-Body Clusters2013

    • Author(s)
      Y. Shigeta, T. Inui, T. Baba, K. Okuno, H. Kuwabara, R. Kishi, M. Nakano
    • Journal Title

      International Journal of Quantum Chemistry

      Volume: 113 Pages: 348-355

  • [Journal Article] Consistent Scheme for Computing Standard Hydrogen Electrode and Redox Potentials2013

    • Author(s)
      T. Matsui, Y. Kitagawa, M. Okumura, Y. Shigeta, S. Sakaki
    • Journal Title

      J. Comp. Chem

      Volume: 34 Pages: 21-26

  • [Journal Article] Density Functional Studies of the Structural Variety of the Cu2S2 Core of the CuA Site2012

    • Author(s)
      Y. Takano, O. Okuyama, Y. Shigeta, H. Nakamura
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 3756-3762

  • [Journal Article] DFT Analysis of Low-Frequency Heme Vibrations in Soluble Guanylate Cyclase : Raman Mode Enhancement by Propionate-Protein Interactions2012

    • Author(s)
      M. Kubo, O. Okuyama, T. Kitagawa, Y. Shigeta
    • Journal Title

      Chem. Lett

      Volume: 41 Pages: 860-862

  • [Journal Article] Tuned CAM-B3LYP Functional in the Time-Dependent Density Functional Theory Scheme for Excitation Energies and Properties of Diarylethene Derivatives2012

    • Author(s)
      K. Okuno, Y. Shigeta, R. Kishi, H. Miyasaka, M. Nakano
    • Journal Title

      J. Photochem. Photobio. A

      Volume: 235 Pages: 29-34

  • [Journal Article] Coordination Effects on the Electronic Structure of the CuA Site of Cytochrome c Oxidase2012

    • Author(s)
      K. Koizumi, Y. Shigeta, O. Okuyama, H. Nakamura, Y. Takano
    • Journal Title

      Chem. Phys. Lett

      Volume: 531 Pages: 197-201

  • [Journal Article] Theoretical Insight into Stereoselective Reaction Mechanisms of 2, 4-Pentanediol-Tethered Ketene-Olefin [2+2] Cycloaddition2012

    • Author(s)
      K. Kamiya, T. Matsui, T. Sugimura, Y. Shigeta
    • Journal Title

      J Phys. Chem. A

      Volume: 116 Pages: 1168-1175

  • [Journal Article] Electronic Structures of the Cu_2S_2 Core of the CuA Site in Cytochrome c Oxidase and Nitronous Oxide Reductase2012

    • Author(s)
      Y. Takano, Y. Shigeta, K. Koizumi, H. Nakamura
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 208-218

  • [Journal Article] Possible Mechanisms of Water Splitting Reaction Based on Proton and Electron Release Pathways Revealed for CaMn_4O_5 Cluster of PSII Refined to 1.9囗 X-Ray Resolution2012

    • Author(s)
      T. Saito, S. Yamanaka, K. Kanda, H. Isobe, Y. Takano, Y. Shigeta, Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya, M. Okumura, M. Shoji, Y. Yoshioka, K. Yamaguchi
    • Journal Title

      Int. J. Quantum Chem

      Volume: 112 Pages: 253-276

  • [Journal Article] An Accurate Density Functional Theory Based Estimation of pKa Values of Polar Residues Combined with Experimental Data : From Amino Acids to Minimal Proteins2012

    • Author(s)
      T. Matsui, T. Baba, K. Kamiya, Y. Shigeta
    • Journal Title

      Phys. Chem. Chem. Phys

      Volume: 14 Pages: 4181-4187

  • [Journal Article] First-principles Molecular Dynamics Studies on the Atomistic Behavior of His503 in Bovine Cytochrome c Oxidase2011

    • Author(s)
      K. Kamiya, Y. Shigeta
    • Journal Title

      Biochim. Biophys. Acta

      Volume: 1807 Pages: 1328-1335

  • [Journal Article] A Theoretical Study on Reaction Scheme of Silver (I) Containing 5-Substituted Uracils Bridge Formation2011

    • Author(s)
      T. Matsui, H. Miyachi, T. Baba, Y. Shigeta
    • Journal Title

      J Phys. Chem. A

      Volume: 115 Pages: 8504-10

  • [Journal Article] Electron Conductivity in Modified Models of Artificial Meta-DNA Using Green's Function-Based Elastic Scattering Theory2011

    • Author(s)
      Y. Nakanishi, T. Matsui, Y. Kitagawa, Y. Shigeta, T. Saito, Y. Kataoka, T. Kawakami, M. Okumura, K. Yamaguchi
    • Journal Title

      Bull. Chem. Soc. Jpn. (Selected Article)

      Volume: 84 Pages: 366-375

  • [Journal Article] Molecular Dynamics Studies on the Mutational Structures of a Nylon-6 Byproduct-Degrading Enzyme2011

    • Author(s)
      T. Baba, K. Kamiya, T. Matsui, N. Shibata, Y. Higuchi, T. Kobayashi, S. Negoro, Y. Shigeta
    • Journal Title

      Chem. Phys. Lett

      Volume: 507 Pages: 157-161

  • [Journal Article] A Simple Scheme for Estimating the pKa Values of 5-Substituted Uracils2011

    • Author(s)
      T. Matsui, A. Oshiyama, Y. Shigeta
    • Journal Title

      Chem. Phys. Lett

      Volume: 502 Pages: 4-6, 248-252

  • [Journal Article] Sequence-Dependent Proton-Transfer Reaction in Stacked GC Pair III : The Influence of Proton Transfer to Conductivity2010

    • Author(s)
      Y. Nakanishi, T. Matsui, Y. Shigeta, Y. Kitagawa, T. Saito, Y. Kataoka, T. Kawakami, M. Okumura, K. Yamaguchi
    • Journal Title

      Int. J. Quantum Chem

      Volume: 110 Pages: 2221-2230

  • [Journal Article] Energy Compensation Mechanism for Charge- Separated Protonation States in Aspartate- Histidine Amino Acid Residue Pairs2010

    • Author(s)
      K. Kamiya, M. Boero, K. Shiraishi, A. Oshiyama, Y. Shigeta
    • Journal Title

      J Phys. Chem. B

      Volume: 114 Pages: 6567-6578

  • [Journal Article] Effects of Mercury (II) on Structural Properties, Electronic Structure and UV Absorption Spectra of Thymine-Mercury(II)-Thymine Nucleobase Pair Containing Duplex2010

    • Author(s)
      H. Miyachi, T. Matsui, Y. Shigeta, K. Hirao
    • Journal Title

      Phys. Chem. Chem. Phys

      Volume: 12 Pages: 909-917

  • [Presentation] 構造ゆらぎと化学反応に関する理論的研究2013

    • Organizer
      分子科学会奨励賞受賞講演
    • Place of Presentation
      京都
    • Year and Date
      20130924-27
  • [Presentation] Free Energy Analyses on Cluster Deformations by Cumulant Mechanics2013

    • Organizer
      8th Congress of the International Society for Theoretical Chemical Physics
    • Place of Presentation
      Budapest, Hungary
    • Year and Date
      20130825-31
  • [Presentation] 第一原理計算に基づく反応解析2013

    • Organizer
      「宇宙生命計算科学連携拠点」ワークショップ
    • Place of Presentation
      筑波大学
    • Year and Date
      20130628-29
  • [Presentation] 量子化学計算によるタンパク質の物性および機能評価2013

    • Organizer
      第13回蛋白質科学会, ワークショップ "蛋白質機能を化学的に理解するために"
    • Place of Presentation
      とりぎん文化会館(鳥取)
    • Year and Date
      20130612-14
  • [Presentation] Theoretical Studies on Current-Voltage (I-V) Characteristics of Metal Containing Artificial DNA and Ni Complex Based Molecular Devices2012

    • Organizer
      2012 Workshop on Innovative Nanoscale Devices and Systems (WINDS)
    • Place of Presentation
      Hapuna Beach Hotel, Hawaii, USA
    • Year and Date
      20121202-07
  • [Presentation] Design of Nylon Oligomer Hydrolase on the Basis of Simulations2012

    • Organizer
      BIT's 3rd Symposium on Enzymes & Biocatalysis 2012
    • Place of Presentation
      Xian, China
    • Year and Date
      20120425-28
  • [Presentation] 第一原理計算に基づく反応解析2012

    • Organizer
      第4回神戸大学協定講座シンポジウム「計算生物学と材料科学の融合」
    • Place of Presentation
      神戸大学
    • Year and Date
      2012-12-19
  • [Presentation] First-principles Analysis on Proton Transport Pathways of Cytochrome c Oxidase2012

    • Organizer
      Asian International Symposium on Theoretical Chemistry 2012
    • Place of Presentation
      Tokyo, Japan
    • Year and Date
      2012-03-26
  • [Presentation] First-principle Analyses on Reaction Mechanisms of Enzymes and Related Topics2011

    • Organizer
      International Conference of Computational Methods in Sciences and Engineering 2011
    • Place of Presentation
      Halkidiki, Greece
    • Year and Date
      20111002-07
  • [Presentation] Classical and Quantal Cumulant Dynamics2011

    • Organizer
      16th International Workshop on Quantum Systems in Chemistry and Physics
    • Place of Presentation
      Ishikawa, Japan
    • Year and Date
      20110911-17
  • [Presentation] Classical Cumulant Dynamics2011

    • Organizer
      7th Congress of the International Society for Theoretical Chemical Physics
    • Place of Presentation
      Tokyo, Japan
    • Year and Date
      20110902-07
  • [Presentation] Theoretical Study on Artificial and Mismatch DNA Bases2010

    • Organizer
      Symposium #5 Pacifichem 2010
    • Place of Presentation
      Hawaii, USA
    • Year and Date
      20101214-20
  • [Presentation] Analyses of Bio-Molecular Reactions Based on First-Principles Calculations2010

    • Organizer
      Frontier in reaction path theory
    • Place of Presentation
      福井謙一記念研究センター・京都大学
    • Year and Date
      2010-09-12
  • [Presentation] 生体内化学反応解析の基礎 : 化学反応理解の為の古典・統計・量子力学

    • Organizer
      分子研量子化学冬の学校
    • Place of Presentation
      分子科学研究所
    • Year and Date
      00001216-17
  • [Presentation] Quantum chemical studies for estimation of pKa and redox potential

    • Organizer
      World Congress on Petrochemistry and Chemical Engineering
    • Place of Presentation
      San Antonio USA
    • Year and Date
      00001117-19
  • [Presentation] Theoretical Studies on Reaction Mechanism of An Enzyme Cleaving Unnatural Amide Compound

    • Organizer
      Symposium on Molecular Science and Synthesis of Functional Molecules for Next Generation
    • Place of Presentation
      Hiroshima, Japan
    • Year and Date
      00000310-11
  • [Book] "Quantal Cumulant Mechanics as Extended Ehrenfest Theorem", Quantum Mechanics, Chap. 172013

    • Author(s)
      Y. Shigeta
    • Publisher
      InTech open
  • [Book] "Theoretical Studies on Metal-Containing Artificial DNA Bases", Advances in the Theory of Atomic and Molecular Systems, Conceptual and Computational Advances in Quantum Chemistry2012

    • Author(s)
      T. Matsui, H. Miyachi, Y. Shigeta
    • Total Pages
      433-460
    • Publisher
      InTech open

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Published: 2015-07-16  

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