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Protein Structure Analysis by Second-order Nonlinear Spectroscopy

Research Project

Project/Area Number 22350014
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Physical chemistry
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

YAMAGUCHI Shoichi  独立行政法人理化学研究所, 田原分子分光研究室, 専任研究員 (60250239)

Co-Investigator(Kenkyū-buntansha) HOSOI Haruko  東邦大学, 理学部, 講師 (00313396)
Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥19,890,000 (Direct Cost: ¥15,300,000、Indirect Cost: ¥4,590,000)
Fiscal Year 2012: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2011: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2010: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
Keywordsタンパク質 / 高次構造 / 配向 / 二次非線形感受率 / 円二色性 / ヘテロダイン検出 / 和周波発生分光 / ポリペプチド / ヘテロダイン検出振動和周波発生分光法 / ヘテロダイン検出電子和周波発生分光法 / セグメント / ヘテロダイン検出電子和周波発生 / パラニトロアニリン / システイン / リシン / Hisタグ / ニッケル修飾ガラス表面
Research Abstract

I show that a newly-developed second-order nonlinear spectroscopic technique allows me to draw topology diagrams of such proteins. Uniquely, one can determine "up" versus "down" alignment of molecules on a surface using this second-order nonlinear spectroscopy. In my novel but simple approach, an "alignment indicator" is introduced to each segment of a protein before immobilizing the protein on a glass surface, and the up versus down alignment of each segment is nonlinear-spectroscopically determined. This approach is very powerful and useful for proteins to which neither X-ray nor NMR is applicable.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (35 results)

All 2013 2012 2011 2010

All Journal Article (25 results) (of which Peer Reviewed: 25 results) Presentation (9 results) (of which Invited: 2 results) Book (1 results)

  • [Journal Article] Computational analysis of the quadrupole contribution in the second-harmonic generation spectroscopy for the water/vapor interface2013

    • Author(s)
      Kazuya Shiratori, Shoichi Yamaguchi, Tahei Tahara, and Akihiro Morita
    • Journal Title

      J. Chem. Phys

      Volume: 138 Pages: 64704-64704

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure and Dynamics of Interfacial Water Studied by Heterodyne-Detected Vibrational Sum-Frequency Generation2013

    • Author(s)
      Satoshi Nihonyanagi, Jahur A. Monda, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      Ann. Rev. Phys. Chem

      Volume: 64 Pages: 579-603

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Quantitative estimate of the water surface pH using heterodyne-detected electronic sum frequency generation2012

    • Author(s)
      Shoichi Yamaguchi, Achintya Kundu, Pratik Sen, and Tahei Tahara
    • Journal Title

      J. Chem. Phys

      Volume: 137 Pages: 151101-151101

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ultrafast vibrational dynamics of water at a charged interface revealed by two-dimensional heterodyne-detected vibrational sum frequency generation2012

    • Author(s)
      Prashant Chandra Singh, Satoshi Nihonyanagi, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      J. Chem. Phys

      Volume: 137 Pages: 94706-94706

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ultrafast Vibrational Dynamics of a Charged Aqueous Interface by Femtosecond Time-Resolved Heterodyne-Detected Sum Frequency Generation2012

    • Author(s)
      Satoshi Nihonyanagi, Prashant Chandra Singh, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      Bull. Chem. Soc. Jpn

      Volume: 85 Pages: 758-760

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Three Distinct Water Structures at a Zwitterionic Lipid/Water Interface Revealed by Heterodyne-Detected Vibrational Sum Frequency Generation2012

    • Author(s)
      Jahur A. Mondal, Satoshi Nihonyanagi, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      J. Am. Chem. Soc

      Volume: 134 Pages: 7842-7850

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Quantitative estimate of the water surface pH using heterodyne-detected electronic sum frequency generation2012

    • Author(s)
      Shoichi Yamaguchi, Achintya Kundu, Pratik Sen, and Tahei Tahara
    • Journal Title

      J. Chem. Phys.

      Volume: 137 Issue: 15 Pages: 1511011-4

    • DOI

      10.1063/1.4758805

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Up' versus 'down' alignment and hydration structures of solutes at the air/water interface revealed by heterodyne-detected electronic sum frequency generation with classical molecular dynamics simulation2011

    • Author(s)
      Shoichi Yamaguchi, Hidekazu Watanabe, Sudip Kumar Mondal, Achintya Kundu, and Tahei Tahara
    • Journal Title

      J. Chem. Phys

      Volume: 135 Pages: 194705-194705

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Unified Molecular View of Air/Water Interface Based on Experimental and Theoretical c^<2> Spectra of Isotopically Diluted Water Surface2011

    • Author(s)
      Satoshi Nihonyanagi, Tatsuya Ishiyama, Touk-kwan Lee, Shoichi Yamaguchi, Mischa Bonn, Akihiro Morita, and Tahei Tahara
    • Journal Title

      J.Am. Chem. Soc

      Volume: 133 Pages: 16875-16880

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Electric quadrupole contribution to the nonresonant background of sum frequency generation at air/liquid interfaces2011

    • Author(s)
      Shoichi Yamaguchi, Kazuya Shiratori, Akihiro Morita, and Tahei Tahara
    • Journal Title

      J. Chem. Phys

      Volume: 134 Pages: 184705-184705

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Acid-Base Equilibrium at an Aqueous Interface: pH Spectrometry by Heterodyne-Detected Electronic Sum Frequency Generation2011

    • Author(s)
      Shoichi Yamaguchi, Kankan Bhattacharyya, and Tahei Tahara
    • Journal Title

      J. Phys. Chem. C

      Volume: 115 Pages: 4168-4173

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecules at the Air/Water Interface Experience a More Inhomogeneous Solvation Environment than in Bulk Solvents: A Quantitative Band Shape Analysis of Interfacial Electronic Spectra Obtained by HD-ESFG2011

    • Author(s)
      Sudip Kumar Mondal, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      J. Phys. Chem. C

      Volume: 115 Pages: 3083-3089

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Acid-Base Equilibrium at an Aqueous Interface : pH Spectrometry by Heterodyne-Detected Electronic Sum Frequency Generation2011

    • Author(s)
      Shoichi Yamaguchi
    • Journal Title

      J.Phys.Chem.C

      Volume: 115 Issue: 10 Pages: 4168-4173

    • DOI

      10.1021/jp1113174

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Electric quadrupole contribution to the nonresonant background of sum frequency generation at air/liquid interfaces2011

    • Author(s)
      Shoichi YAMAGUCHI, Kazuya SHIRATORI, Akihiro MORITA, Tahei TAHARA
    • Journal Title

      J.Chem.Phys.

      Volume: 134 Issue: 18 Pages: 184705-184705

    • DOI

      10.1063/1.3586811

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] "Up" versus "down" alignment and hydration structures of solutes at the air/water interface revealed by heterodyne-detected electronic sum frequency generation with classical molecular dynamics simulation2011

    • Author(s)
      Shoichi YAMAGUCHI, Hidekazu WATANABE, Sudip Kumar MONDAL.KUNDU, Tahei TAHARA
    • Journal Title

      J.Chem.Phys

      Volume: 135 Issue: 19 Pages: 194705-194705

    • DOI

      10.1063/1.3662136

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Physisorption Gives Narrower Orientational Distribution than Chemisorption on a Glass Surface: A Polarization-Sensitive Linear and Nonlinear Optical Study2010

    • Author(s)
      Shoichi Yamaguchi, Haruko Hosoi, Megumi Yamashita, Pratik Sen, and Tahei Tahara
    • Journal Title

      J. Phys. Chem. Lett

      Volume: 1 Pages: 2662-2665

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure and orientation of water at charged lipid monolayer/water interfaces probed by heterodyne-detected vibrational sum frequency generation spectroscopy2010

    • Author(s)
      Jahur A. Mondal, Satoshi Nihonyanagi, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      J. Am. Chem. Soc

      Volume: 132 Pages: 10656-10657

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Water Hydrogen Bond Structure near Highly Charged Interfaces Is Not Like Ice2010

    • Author(s)
      Satoshi Nihonyanagi, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      J. Am. Chem. Soc

      Volume: 132 Pages: 6867-6869

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Half hydration' at the air/water interface revealed by heterodyne-detected electronic sum frequency generation spectroscopy, polarization second harmonic generation, and molecular dynamics simulation2010

    • Author(s)
      Hidekazu Watanabe, Shoichi Yamaguchi, Sobhan Sen, Akihiro Morita, and Tahei Tahara
    • Journal Title

      J. Chem. Phys

      Volume: 132 Pages: 144701-144701

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ultrafast dynamics of malachite green at the air/water interface studied by femtosecond time-resolved electronic sum frequency generation (TR-ESFG): an indicator for local viscosity2010

    • Author(s)
      Pratik Sen, Shoichi Yamaguchi, and Tahei Tahara
    • Journal Title

      Faraday Discuss

      Volume: 145 Pages: 411-428

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Ultrafast dynamics of malachite green at the air/water interface studied by femtosecond time-resolved electronic sum frequency generation (TR-ESFG) : an indicator for local viscosity2010

    • Author(s)
      Pratik Sen
    • Journal Title

      Faraday Discuss.

      Volume: 145 Pages: 411-428

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Physisorption Gives Narrower Orientational Distribution than Chemisorption on a Glass Surface : A Polarization-Sensitive Linear and Nonlinear Optical Study2010

    • Author(s)
      Shoichi Yamaguchi
    • Journal Title

      J.Phys.Chem.Lett.

      Volume: 1 Pages: 2662-2665

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 'Half hydration' at the air/water interface revealed by heterodyne-detected electronic sum frequency generation spectroscopy, polarization second harmonic generation, and molecular dynamics simulation2010

    • Author(s)
      Hidekazu Watanabe
    • Journal Title

      J.Chem.Phys.

      Volume: 132 Pages: 144701-144701

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Water Hydrogen Bond Structure near Highly Charged Interfaces Is Not Like Ice2010

    • Author(s)
      Satoshi Nihonyanagi
    • Journal Title

      J.Am.Chem.Soc.

      Volume: 132 Pages: 6867-6869

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and orientation of water at charged lipid monolayer/water interfaces probed by heterodyne-detected vibrational sum frequency generation spectroscopy2010

    • Author(s)
      Jahur A.Mondal
    • Journal Title

      J.Am.Chem.Soc.

      Volume: 132 Pages: 10656-10657

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Interface-Selective Heterodyne-Detected Second-Order Nonlinear Spectroscopy2013

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      CRC International Symposium. New Challenges on the Bio-interfaces: Structures and Dynamics
    • Place of Presentation
      北海道大学,札幌市
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Interface-Selective Heterodyne-Detected Second-Order Nonlinear Vibrational Spectroscopy2012

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      23rd International Conference on Raman Spectroscopy (ICORS)
    • Place of Presentation
      Bangalore, India
    • Year and Date
      2012-08-12
    • Related Report
      2012 Final Research Report
  • [Presentation] Nonlinear Laser Spectroscopy for Surfaces and Interfaces of Liquids", Oral Presentation,2012

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      CAS-RIKEN Frontier Science Workshop 2012
    • Place of Presentation
      Oiso,Japan
    • Year and Date
      2012-05-26
    • Related Report
      2012 Final Research Report
  • [Presentation] Interface-Selective Heterodyne-Detected Second-Order Nonlinear Vibrational Spectroscopy2012

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      23rd International Conference on Raman Spectroscopy
    • Place of Presentation
      Bangalore, India
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Interface-Selective Heterodyne-Detected Second-Order Nonlinear Spectroscopy2011

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      15th East Asian Workshop on Chemical Dynamics
    • Place of Presentation
      Pohang, South Korea
    • Year and Date
      2011-05-20
    • Related Report
      2012 Final Research Report
  • [Presentation] Interface-Selective Heterodyne-Detected Second-Order Nonlinear Spectroscopy2011

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      15th East Asian Workshop on Chemical Dynamics
    • Place of Presentation
      Pohang, South Korea(招待講演)
    • Year and Date
      2011-05-19
    • Related Report
      2011 Annual Research Report
  • [Presentation] 界面選択的なヘテロダイン検出和周波発生分光2010

    • Author(s)
      山口祥一
    • Organizer
      高分子表面研究会
    • Place of Presentation
      東京理科大学,東京
    • Year and Date
      2010-10-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] "Interface-Selective Even-Order Nonlinear Spectroscopy2010

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      The 3rd Asia-Pacific Symposium on Radiation Chemistry
    • Place of Presentation
      Lonavala, India.
    • Year and Date
      2010-09-14
    • Related Report
      2012 Final Research Report
  • [Presentation] Interface-Selective Even-Order Nonlinear Spectroscopy2010

    • Author(s)
      Shoichi Yamaguchi
    • Organizer
      The 3rd Asia-Pacific Symposium on Radiation Chemistry
    • Place of Presentation
      Lonavala, India
    • Year and Date
      2010-09-14
    • Related Report
      2010 Annual Research Report
  • [Book] 高効率二光子吸収材料の開発と応用第4章2節"二光子吸収材料の非線形光学スペクトル測定"2011

    • Author(s)
      山口祥一
    • Publisher
      シーエムシー出版
    • Related Report
      2011 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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