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A NMR Study of Individual Residues of Proteins in a Random Coil State

Research Project

Project/Area Number 19540431
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics/Chemical physics
Research InstitutionKwansei Gakuin University

Principal Investigator

NODA Yasuo  Kwansei Gakuin University, 理工学部, 教育技術主事 (40268511)

Co-Investigator(Kenkyū-buntansha) SEGAWA Shin-ichi  関西学院大学, 理工学部, 教授 (70103132)
Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2009: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2008: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2007: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords生物物理 / タンパク質 / リゾチーム / 核磁気共鳴 / ジスルフィド結合 / ランダムコイル / 重水素交換 / ジメチルスルホキシド
Research Abstract

2SS[6-127, 64-80] variant of lysozyme which has two disulfide bridges and lacks the other two disulfide bridges was quite unstructured in water, but a part of the polypeptide chain was gradually frozen into a native-like conformation with increasing glycerol concentration. It was monitored from the protection factors of amide hydrogens against H/D exchange by means of NMR spectroscopy. With increasing glycerol concentration, some selected regions were further protected. The highly protected residues were included in A-, Band C-helices and β3-strand, and especially centered on Ile 55 and Leu 56. In 2SS[6-127, 64-80], long-range interactions were recovered due to the preferential hydration by glycerol in the hydrophobic box of the α-domain.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (33 results)

All 2010 2009 2008 2007 Other

All Journal Article (7 results) (of which Peer Reviewed: 7 results) Presentation (24 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Glycerol-Induced Folding of Unstructured Disulfide-Deficient Lysozyme into a Native-Like Conformation2009

    • Author(s)
      Sakamoto, K., Hirai, K., Kitamura, Y., Yamazaki, K., Yusa, M., Tokunaga, N., Doi, G., Noda, Y., Tachibana, H., Segawa, S
    • Journal Title

      Biopolymers 91

      Pages: 665-675

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Glycerol-Induced Folding of Unstructured Disulfide-Deficient Lysozyme into a Native-Like Conformation.2009

    • Author(s)
      Sakamoto, K.
    • Journal Title

      Biopolymers 91

      Pages: 665-675

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Confirmation of the Denatured Structure of Pyrrolidone Carboxyl Peptidase under Nondenaturing Conditions: Difference in Helix Propensity of Two Synthetic Peptides with Single Amino Acid Substitution2008

    • Author(s)
      Umezaki, T., Iimura, S., Noda, Y., Segawa, S., Yutani, K
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics 71

      Pages: 737-742

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The confirmation of the denatured structure of pyrrolidone carboxyl peptidase under nondenaturing conditions : difference in helix propensity of two synthetic peptides with single amino acid substitution.2008

    • Author(s)
      Umezaki T
    • Journal Title

      Proteins : Structure, Function, and Bioinformatics 71

      Pages: 737-742

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The confiemation of the denatured structure of pyrrolidone carboxyl peptidase under nondenaturing conditions:difference in helix propensity of two synthetic peptides with single amino acid substitution2008

    • Author(s)
      Umezaki T
    • Journal Title

      Proteins:Structure, Function, and Bioinformatics 71

      Pages: 737-742

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of the Denatured Structure of Pyrrolidone Carboxyl Peptidase from a Hyperthermophile under Nondenaturing Conditions: Role of the C-Terminalα-Helix of the Protein in Folding and Stability2007

    • Author(s)
      Iimura, S., Umezaki, T., Takeuchi, M., Mizuguchi, M., Yagi, H., Ogasahara, K., Akutsu, H., Noda, Y., Segawa, S., Yutani, K
    • Journal Title

      Biochemistry 46

      Pages: 3664-3672

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Characterization of the denatured structure of pyrrolidone carboxyl peptidase from a hyperthermophile under nondenaturing conditions:role of the C-terminal α-helix of the protein in folding and stability2007

    • Author(s)
      Limura S
    • Journal Title

      Biochemistry 46

      Pages: 3664-3672

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] NMR分光法を用いたジスルフィド結合を欠損させたデンプン結合ドメインのリフォールディング中間体の構造解析2010

    • Author(s)
      杉本華幸、野田康夫、瀬川新一
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      東京大学駒場キャンパス
    • Year and Date
      2010-03-29
    • Related Report
      2009 Final Research Report
  • [Presentation] NMR分光法を用いたジスルフィド結合を欠損させたデンプン結合ドメインのリフォールディング中間体の構造解析2010

    • Author(s)
      杉本華幸
    • Organizer
      日本農芸化学会
    • Place of Presentation
      東京大学駒場キャンパス
    • Year and Date
      2010-03-29
    • Related Report
      2009 Annual Research Report
  • [Presentation] モルテングロビュール段階で見出されるPCP(ピロリドンカルボキシルペプチダーゼ)の逐次折れたたみ経路とそれに続く天然構造への転移(Sequential folding pathway of PCP(Pyrrolidone Carboxyl Peptidase) found in the molten-globule-like stage and the following folding transition)2009

    • Author(s)
      横田洋平、キンマンクリストファー、藪本和義、野田康夫、油谷克英、瀬川新一
    • Organizer
      第47回日本生物物理学会
    • Place of Presentation
      スティとくしま
    • Year and Date
      2009-10-30
    • Related Report
      2009 Final Research Report
  • [Presentation] リゾチームのs-s結合欠損変異体における残留非ランダム構造(Residual Nonrandom Structures in Disulfide-Deficient Variants of Lysozyme)2009

    • Author(s)
      笠井健一、奈良間邦成、野田康夫、橘秀樹、瀬川新一
    • Organizer
      第47回日本生物物理学会
    • Place of Presentation
      アスティとくしま
    • Year and Date
      2009-10-30
    • Related Report
      2009 Final Research Report
  • [Presentation] リゾチームのS-S結合欠損変異体における残留非ランダム構造2009

    • Author(s)
      笠井健一
    • Organizer
      日本生物物理学会
    • Place of Presentation
      アスティとくしま
    • Year and Date
      2009-10-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] モルテングロビュール段階で見出されるPCP(ピロリドンカルボキシルペプチダーゼ)の逐次折れたたみ経路とそれに続く天然構造への転移2009

    • Author(s)
      横田洋平
    • Organizer
      日本生物物理学会
    • Place of Presentation
      アスティとくしま
    • Year and Date
      2009-10-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] NMR analysis of intermediate in thermal unfolding process of mouse lipocalin-type prostaglandin D synthase2009

    • Author(s)
      宮本優也、野田康夫、西村重徳、猿渡馨、瀬川新一、乾隆
    • Organizer
      第82回日本生化学会大会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2009-10-22
    • Related Report
      2009 Final Research Report
  • [Presentation] NMR analysis of a kinetically trapped refolding intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase2009

    • Author(s)
      杉本華幸、野田康夫、瀬川新一
    • Organizer
      第82回日本生化学会大会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2009-10-22
    • Related Report
      2009 Final Research Report
  • [Presentation] ジスルフィド結合を欠損させたデンプン結合ドメインのリフォールディング中間体のNMRによる解析2009

    • Author(s)
      杉本華幸
    • Organizer
      日本生化学会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2009-10-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] NMR法を用いたマウスリポカリン型プロスタグランジンD合成酵素の熱変性中間体の解析2009

    • Author(s)
      宮本優也
    • Organizer
      日本生化学会
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2009-10-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Glycerol-Induced Folding of Unstructured Disulfide-Deficient Lysozyme into a Native-Like Conformation2009

    • Author(s)
      Yasuo Noda
    • Organizer
      Molecular Science of Fluctuations toward Biological Functions and Chemistry of Biological Processes Created by Water and Biomolecules Okazaki Conference Center
    • Place of Presentation
      Japan
    • Year and Date
      2009-05-16
    • Related Report
      2009 Final Research Report
  • [Presentation] Glycerol-Induced Folding of Unstructured Disulfide-Deficient Lysozyme into a Native-Like Conformation2009

    • Author(s)
      Yasuo Noda
    • Organizer
      Molecular Science of Fluctuations toward Biological Functions and Chemistry of Biological Processes Created by Water and Biomolecules
    • Place of Presentation
      Okazaki Conference Center, Japan
    • Year and Date
      2009-03-16
    • Related Report
      2008 Annual Research Report
  • [Presentation] 1H-NMRを用いたリポカリン型プロスタグランジンD合成酵素の熱変性中間体の解析(1H-NMR analysis of intermediate in the thermal unfolding process of lipocalin-type prostaglandin D Synthase)2008

    • Author(s)
      宮本優也、野田康夫、西村重徳、猿渡馨、瀬川新一、乾隆
    • Organizer
      第81回日本生化学会大会
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-09
    • Related Report
      2009 Final Research Report
  • [Presentation] モルテングロビュール状の変性状態においてピロリドンカルボキシルペプチダーゼ(PCP)の折りたたみ反応は順次進行していく(The folding of PCP(Pyrrolidone Carboxyl Peptidase) sequentially proceeds in the denatured state similar to the stage of molten globule)2008

    • Author(s)
      横田洋平、吉田篤史、野田康夫、油谷克英、瀬川新一
    • Organizer
      第46回日本生物物理学会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2008-12-05
    • Related Report
      2009 Final Research Report
  • [Presentation] モルテングロビュール状の変性状態においてピロリドンカルボキシルペプチダーゼ(PCP)の折りたたみ反応は順次進行していく2008

    • Author(s)
      横田洋平
    • Organizer
      日本生物物理学会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2008-12-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] n-アセチルグルコサミン3量体結合によって、リゾチーム変異体2ss(1+3)、2ss(3+4)、2ss(1+2)に誘導される秩序構造(Structures induced by tri-NAG binding to 2SS(1+3), 2SS(3+4) and 2SS(1+2) variants of lysozyme)2008

    • Author(s)
      吉田篤史、笠井健一、野田康夫、橘秀樹、瀬川新一
    • Organizer
      第46回日本生物物理学会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2008-12-04
    • Related Report
      2009 Final Research Report
  • [Presentation] N-アセチルグルコサミン3量体結合によって、リゾチーム変異体2SS(1+3)、2SS(3+4)、2SS(1+2)に誘導される秩序構造2008

    • Author(s)
      吉田篤史
    • Organizer
      日本生物物理学会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2008-12-04
    • Related Report
      2008 Annual Research Report
  • [Presentation] リゾチーム1SS変異体の部分秩序構造形成に対するグリセロールの影響(Effects of glycerol on the formation of partially ordered structures in 1SS-variants of lysozyme)2007

    • Author(s)
      村上周作、徳永直紀、野田康夫、橘秀樹、瀬川新一
    • Organizer
      第45回日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2009 Final Research Report
  • [Presentation] リゾチームの1SS-、2SS-変異体のS-S結合再生反応のキネティックス(Kinetic studies of disulfide regeneration of 1SS- or 2SS-variants of lysozyme)2007

    • Author(s)
      松尾和宏、野田康夫、橘秀樹、瀬川新一
    • Organizer
      第45回日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2009 Final Research Report
  • [Presentation] 構造を失ったリゾチーム2ss変異体に誘起される秩序構造(Ordered conformation induced in unstructured 2SS-variants of lysozyme)2007

    • Author(s)
      徳永直紀、吉田篤史、野田康夫、橘秀樹、瀬川新一
    • Organizer
      第45回日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2009 Final Research Report
  • [Presentation] 超好熱菌由来タンパク質PCP-0SHの変性初期過程における構造のゆらぎの解明(Structural fluctuation in the folded structure of PCP-0SH at the initial stage of unfolding)2007

    • Author(s)
      梅嵜太郎、飯村哲史、野田康夫、油谷克英、瀬川新一
    • Organizer
      第45回日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-23
    • Related Report
      2009 Final Research Report
  • [Presentation] 構造を失ったリゾチーム2SS変異体に誘起される秩序構造2007

    • Author(s)
      徳永 直紀
    • Organizer
      日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] リゾチーム1SS変異体の部分秩序構造形成に対するグリセロールの影響2007

    • Author(s)
      村上 周作
    • Organizer
      日本生物物理学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2007-12-22
    • Related Report
      2007 Annual Research Report
  • [Presentation] 超好熱菌由来Pyrrolidone carboxyl peptidaseの野生型と変異体A119Pの立体構造と変性機構の比較(Difference of native structure and unfolding mechanism between pyrrolidone carboxyl peptidase from a hyperthermophile and its mutant A119P)2007

    • Author(s)
      飯村哲史、梅嵜太郎、坂本恵子、岡崎伸生、竹内誠、水口峰之、小笠原京子、野田康夫、瀬川新一、油谷克英
    • Organizer
      第7回日本蛋白質科学会
    • Place of Presentation
      仙台国際センター
    • Year and Date
      2007-05-26
    • Related Report
      2009 Final Research Report
  • [Book] タンパク質の事典2008

    • Author(s)
      瀬川新一, 他
    • Publisher
      朝倉書店
    • Related Report
      2009 Final Research Report
  • [Remarks] BMRBデータベース(Biological Magnetic Resonance Data Bank: A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules)BMRB accession number(1)0SS変異体: 11051(2)2SS[6-127,64-80]変異体: 11052

    • Related Report
      2009 Final Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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