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Roles of solvent particles in effective interactions between charged protein and phase behavior under weak coupling condition

Research Project

Project/Area Number 15K05249
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionKyushu University

Principal Investigator

Akiyama Ryo  九州大学, 理学研究院, 准教授 (60363347)

Co-Investigator(Kenkyū-buntansha) 吉森 明  新潟大学, 自然科学系, 教授 (90260588)
徳永 健  工学院大学, 教育推進機構(公私立大学の部局等), 准教授 (30467873)
Research Collaborator Suematsu Ayumi  
Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2017: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords電解質溶液 / 荷電タンパク質溶液 / 液体の積分方程式理論 / 実効相互作用 / DLVO理論 / シミュレーション / コロイド分散系 / サンプリング方法 / 荷電巨大分子 / 分子シミュレーション / 電気二重層斥力 / クーロン系 / 相挙動 / 溶媒の粒子性 / 積分方程式理論 / 粗視化シミュレーション / 平衡クラスター
Outline of Final Research Achievements

The effective interactions between like-charged macromolecules in an electrolyte solution has been investigated using the linearized Poisson-Boltzmann equation (ex. the Debye-Huckel theory). In the present study, the integral equation theory of the liquid (HNC-OZ theory) was used to determine the effective interaction between like-charged macromolecules under conditions where the Debye-Huckel theory becomes worse, namely the Intermediate region. We found that when the ion intensity is the same and the valence number of the coions is different, the distance property is different. These results are qualitatively different from the results in the Debye Huckel region above. Also, this result corresponds qualitatively to the experimental result.

Academic Significance and Societal Importance of the Research Achievements

学術的な意義として、クーロン相互作用よりも熱エネルギーが優勢な条件で、イオンの粒子性や価数を考慮した場合の同符号巨大荷電分子間実効相互作用の計算が行われたことが大きい。これまで、クーロン相互作用が十分に優勢な真逆とも言える条件で計算を行ってきたが、そこから従来よく理解されているデバイーヒュッケル理論が妥当な領域までの間を繋げられたことに意義がある。また共イオンの排斥が起きていると思われる結果は興味深い点になり、今回の計算結果を軸にした分子シミュレーションなどが期待される。また、凝集のためのサンプリング法が見えてきたので、相挙動研究の足がかりをつかめた事も大きな収穫である。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (55 results)

All 2018 2017 2016 2015

All Journal Article (7 results) (of which Peer Reviewed: 7 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (46 results) (of which Int'l Joint Research: 12 results,  Invited: 9 results) Book (2 results)

  • [Journal Article] Effective potential between negatively charged patches on acidic proteins immersed in various electrolyte solutions2018

    • Author(s)
      Suematsu Ayumi、Sawayama Takuto、Akiyama Ryo
    • Journal Title

      The Journal of Chemical Physics

      Volume: 149 Issue: 7 Pages: 074105-074105

    • DOI

      10.1063/1.5038912

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Theoretical approaches for dynamical ordering of biomolecular systems2018

    • Author(s)
      Okumura Hisashi、Higashi Masahiro、Yoshida Yuichiro、Sato Hirofumi、Akiyama Ryo
    • Journal Title

      Biochimica et Biophysica Acta(BBA) - General Subjects

      Volume: 1862 Issue: 2 Pages: 212-228

    • DOI

      10.1016/j.bbagen.2017.10.001

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Basic Cell Size Dependence of Displacement for a Solvation Motor in a Lennard-Jones Solvent2018

    • Author(s)
      Tokunaga Ken, Akiyama Ryo
    • Journal Title

      Journal of Computer Chemistry, Japan

      Volume: 17 Issue: 1 Pages: 80-84

    • DOI

      10.2477/jccj.2018-0004

    • NAID

      130006555812

    • ISSN
      1347-1767, 1347-3824
    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Stick boundary condition at large hard sphere arising from effective attraction in binary hard-sphere mixtures2018

    • Author(s)
      Nakamura Yuka, Yoshimori Akira, Akiyama Ryo, Yamaguchi Tsuyoshi
    • Journal Title

      THE JOURNAL OF CHEMICAL PHYSICS

      Volume: 148 Issue: 12 Pages: 124502-124502

    • DOI

      10.1063/1.5025202

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Electrostatic double-layer interaction between stacked charged bilayers2017

    • Author(s)
      Hishida Mafumi, Nomura Yoko, Akiyama Ryo, Yamamura Yasuhisa, Saito Kazuya
    • Journal Title

      PHYSICAL REVIEW E

      Volume: 96 Issue: 4 Pages: 040601-040601

    • DOI

      10.1103/physreve.96.040601

    • NAID

      120007134697

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Isotactic poly(4-methyl-1-pentene) melt as a porous liquid: Reduction of compressibility due to penetration of pressure medium2017

    • Author(s)
      Chiba Ayano、Inui Masanori、Kajihara Yukio、Fuchizaki Kazuhiro、Akiyama Ryo
    • Journal Title

      THE JOURNAL OF CHEMICAL PHYSICS

      Volume: 146 Issue: 19 Pages: 194503-194503

    • DOI

      10.1063/1.4983508

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Effects of interactions between depletants in phase diagrams of binary hard-sphere systems2016

    • Author(s)
      A. Suematsu, A. Yoshimori and R. Akiyama
    • Journal Title

      EPL (Europhysics Letters)

      Volume: 116 Issue: 3 Pages: 38004-38004

    • DOI

      10.1209/0295-5075/116/38004

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] 大きさの異なる粒子を含む剛体球系の動径分布関数2018

    • Author(s)
      中村有花, 荒井翔太, 秋山良, 吉森明, 木下正弘
    • Organizer
      日本物理学会2018年秋季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 剛体球の動径分布関数から計算する大きな粒子の拡散係数2018

    • Author(s)
      中村有花, 吉森明, 秋山良, 荒井翔太, 木下正弘
    • Organizer
      日本物理学会2018年秋季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 基礎セミナー2「生物物理に理論は必要か」2018

    • Author(s)
      吉森明
    • Organizer
      第58回生物物理若手の会 夏の学校, ぼくらの生物物理の教科書
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 多価カチオンを含む電解質中におけるタンパク質表面の負に帯電した酸素間の実行相互作用2018

    • Author(s)
      末松安由美、菱田真史、秋山良
    • Organizer
      日本物理学会第73回年次大会
    • Related Report
      2017 Research-status Report
  • [Presentation] 溶媒の密度分布で決まる粒子表面の境界条件2018

    • Author(s)
      中村有花, 吉森明, 秋山良, 山口毅
    • Organizer
      日本物理学会第73回年次大会
    • Related Report
      2017 Research-status Report
  • [Presentation] 荷電脂質膜が作る多重層ベシクルの表面電位2018

    • Author(s)
      菱田真史, 秋山良, 山村泰久, 齋藤一弥
    • Organizer
      日本物理学会第73回年次大会
    • Related Report
      2017 Research-status Report
  • [Presentation] 荷電コロイド粒子の結晶化に影響する平均力ポテンシャルの斥力2018

    • Author(s)
      田村雄大, 末松安由美, 吉森明, 秋山良
    • Organizer
      日本物理学会第73回年次大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Effective attraction between negatively charged oxygen atoms on protein surface in an electrolyte solution2018

    • Author(s)
      Ryo Akiyama, Ayumi Suematsu
    • Organizer
      新学術領域研究「動的秩序と機能」第6回国際シンポジウム
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] 蛋白質の結晶化に対する理論的手法の開発2017

    • Author(s)
      田村雄大、吉森明、末松安由美、秋山良
    • Organizer
      「水和とATPエネルギー」研究会
    • Place of Presentation
      秋保、仙台
    • Year and Date
      2017-03-05
    • Related Report
      2016 Research-status Report
  • [Presentation] SIMULATIONS OF LIKE-CHARGED MACROIONS IN AN ELECTROLYTE SOLUTION BASED ON THE EFFECTIVE INTERACTION2017

    • Author(s)
      Ayumi Suematsu, Ryo Akiyama
    • Organizer
      The 5 th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
    • Place of Presentation
      Universiry of Tokyo, Tokyo, Japan
    • Year and Date
      2017-01-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 2成分剛体球系での固体表面への分子吸着における活性化自由エネルギー及び吸着量のモル分率依存性2017

    • Author(s)
      大島 章生、秋山 良
    • Organizer
      凝縮系の理論化学2017
    • Related Report
      2017 Research-status Report
  • [Presentation] 統計力学的手法による2成分剛体球系の相挙動の研究2017

    • Author(s)
      末松安由美、吉森輝、秋山良
    • Organizer
      凝縮系の理論化学2017
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Selectivity of large hard sphere on a hard wall immersed in binary hard-sphere fluid2017

    • Author(s)
      Akio Oshima, Ayano Chiba, Ryo Akiyama
    • Organizer
      The 10th Liquid Matter Conference
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Effective potential and crystallization by depletion effect in binary hard-sphere systems2017

    • Author(s)
      Ayumi Suematsu, Akira Yoshimori, Ryo Akiyama
    • Organizer
      The 10th Liquid Matter Conference
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Statistical Mechanics Study of Reentrant Phase Behavior of Proteins in an Electrolyte Solution2017

    • Author(s)
      Ryo Akiyama
    • Organizer
      The 17th KIAS Conference on Protein Structure and Function
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Exclusion of coions from space between two macroions in an electrolyte solution: the charge dependence2017

    • Author(s)
      A. Suematsu, R. Akiyama and M. Hishida
    • Organizer
      11th Mini Symposium on liquids
    • Related Report
      2017 Research-status Report
  • [Presentation] System Size Dependence of the Motion of Solvation Motor2017

    • Author(s)
      Ken Tokunaga, Ryo Akiyama
    • Organizer
      11th Mini Symposium on liquids
    • Related Report
      2017 Research-status Report
  • [Presentation] Short and long range effects of an effective ectiveg range effects of an effective force on crystallization of like-charged colloidal particles2017

    • Author(s)
      Y. Tamura, A. Suematsu, A. Yoshimori, R. Akiyama
    • Organizer
      11th Mini Symposium on liquids
    • Related Report
      2017 Research-status Report
  • [Presentation] マクロアニオン間の実効相互作用と凝集挙動2017

    • Author(s)
      秋山良
    • Organizer
      「水和とATPエネルギー」研究会
    • Place of Presentation
      秋保、仙台
    • Related Report
      2016 Research-status Report
  • [Presentation] 空隙のある高分子結晶P4MP1およびsPSへの分子吸蔵(II)2017

    • Author(s)
      千葉文野、折戸朗子、秋山良
    • Organizer
      日本物理学会第72回年次大会
    • Place of Presentation
      大阪大学豊中キャンパス、大阪
    • Related Report
      2016 Research-status Report
  • [Presentation] Appearance and Disappearance of Strong Attraction between Negatively Charged Macromolecules in an Electrolyte Solution2016

    • Author(s)
      Ryo Akiyama
    • Organizer
      The 4th International Kyushu Colloid Colloquium
    • Place of Presentation
      Kyusyu University, Fukuoka, Japan
    • Year and Date
      2016-09-27
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 巨大分子を使った寄木細工の為の方針の2つ2016

    • Author(s)
      秋山良
    • Organizer
      『分子を使った寄せ木細工』:自己組織化したソフトマテリアルが織り成す『かたち』と機能
    • Place of Presentation
      島根大学教育学部(島根県松江市)
    • Year and Date
      2016-05-27
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] 同符号コロイド粒子間相互作用における同符号イオンの価数依存性2016

    • Author(s)
      山下拓海、秋山 良
    • Organizer
      日本物理学会 第71回年次大会
    • Place of Presentation
      仙台
    • Year and Date
      2016-03-19
    • Related Report
      2015 Research-status Report
  • [Presentation] 電解質溶液中で働く強い同符号荷電間実効引力の理論的研究とタンパク質の凝集挙動2016

    • Author(s)
      秋山良
    • Organizer
      福岡大学化学科談話会
    • Place of Presentation
      福岡大学(福岡市)
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] HNC-OZ理論による電解質溶液中同符号コロイド粒子間相互作用に基づくモンテカルロシミュレーション2016

    • Author(s)
      末松安由美、秋山良
    • Organizer
      日本物理学会2016年秋季大会
    • Place of Presentation
      金沢大学(金沢市)
    • Related Report
      2016 Research-status Report
  • [Presentation] 空隙のある高分子結晶P4MP1およびsPSへの分子吸蔵2016

    • Author(s)
      千葉文野、 秋山良
    • Organizer
      日本物理学会2016年秋季大会
    • Place of Presentation
      金沢大学(金沢市)
    • Related Report
      2016 Research-status Report
  • [Presentation] Radial distribution function of interaction between the charged colloid particles obtained by the Montecarlo simulation using effective interaction calculated by the HNC-OZ theory2016

    • Author(s)
      Ayumi Suematsu, Ryo Akiyama
    • Organizer
      The 10th Mini-Symposium on Liquids
    • Place of Presentation
      Okayama University, Okayama, Japan
    • Related Report
      2016 Research-status Report
  • [Presentation] 積分方程式理論で計算した電解質溶液中の同符号荷電粒子間実効 相互作用2016

    • Author(s)
      秋山良
    • Organizer
      第6回ソフトマター研究会
    • Place of Presentation
      北海道大学、札幌
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] Molecular simulation of macroanions in an electrolyte solution based on the effective potential2016

    • Author(s)
      Ayumi Suematsu, Ryo Akiyama
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場、つくば
    • Related Report
      2016 Research-status Report
  • [Presentation] 電解質溶液中の同符号荷電コロイド粒子間実効引力と蛋白質溶液の相図2015

    • Author(s)
      秋山 良
    • Organizer
      慶応義塾大学理工学部物理学科談話会
    • Place of Presentation
      横浜
    • Year and Date
      2015-11-24
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Effective attraction between negatively charged sites on proteins and ordering of proteins in an electrolyte solution2015

    • Author(s)
      Ryo Akiyama
    • Organizer
      The 4th International Symposium “Dynamical Ordering of Biomolecular Systems for creation of integrated functions”(新学術領域研究『動的秩序と機能』第4回国際シンポジウム)
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-11-22
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Aggregation of acidic proteins and effective attraction between like-charged particles2015

    • Author(s)
      Takuto Sawayama, Ryo Akiyama
    • Organizer
      The 4th International Symposium “Dynamical Ordering of Biomolecular Systems for creation of integrated functions”(新学術領域研究『動的秩序と機能』第4回国際シンポジウム)
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-11-22
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Effects of depletion interaction on the crystallization
2015

    • Author(s)
      Ayumi Suematsu, Akira Yoshimori, Ryo Akiyama
    • Organizer
      The 4th International Symposium “Dynamical Ordering of Biomolecular Systems for creation of integrated functions”(新学術領域研究『動的秩序と機能』第4回国際シンポジウム)
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-11-22
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Dependence of effective interaction between macroanions in electrolyte solution on valence of co-ions2015

    • Author(s)
      Takumi Yamashita, Ryo Akiyama
    • Organizer
      The 4th International Symposium “Dynamical Ordering of Biomolecular Systems for creation of integrated functions”(新学術領域研究『動的秩序と機能』第4回国際シンポジウム)
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-11-22
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 電解質溶液中のマクロアニオン間実効相互作用に同符号イオンの価数が与える効果2015

    • Author(s)
      山下拓海、秋山良
    • Organizer
      第38回溶液化学シンポジウム
    • Place of Presentation
      高知
    • Year and Date
      2015-10-21
    • Related Report
      2015 Research-status Report
  • [Presentation] 電解質溶液内におけるマクロアニオン凝集の相図の計算2015

    • Author(s)
      澤山拓斗、秋山良
    • Organizer
      第38回溶液化学シンポジウム
    • Place of Presentation
      高知
    • Year and Date
      2015-10-21
    • Related Report
      2015 Research-status Report
  • [Presentation] Spatiotemporal dynamic ordering regulated by ATP hydrolysis and effective attraction between negatively charged sites in a biofluid, International2015

    • Author(s)
      Ryo Akiyama
    • Organizer
      The 53rd Annual Meeting of the Biophysical Society of Japan, Formation of spatiotemporal dynamic ordering mediated by ATP hydrolysis (新学術 領域研究『動的秩序と機能』共催シンポジウム)
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] Aggregation behavior of macroanions immersed in electrolyte solution2015

    • Author(s)
      Takuto Sawayama, Ryo Akiyama
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] Effects of Preferential Solvation on Partial Molar Enthalpies in Binary Mixture Systems: Molecular Simulation Study2015

    • Author(s)
      Yuichi Kawabata, Ryo Akiyama
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] マクロアニオン間相互作用に対する同符号小イオンの価数依存性2015

    • Author(s)
      山下拓海、秋山良
    • Organizer
      第66回コロイドおよび界面化学討論会
    • Place of Presentation
      鹿児島
    • Year and Date
      2015-09-11
    • Related Report
      2015 Research-status Report
  • [Presentation] Effects of Co-ions with Different Valences on Effective Interaction between Macroanions in an Electrolyte Solution2015

    • Author(s)
      Takumi Yamashita, Ryo Akiyama
    • Organizer
      2015 International Conference of Colloids and Interface Science
    • Place of Presentation
      Taipei
    • Year and Date
      2015-07-21
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Phase behavior of Acidic Protein electrolyte solution: Theoretical approach with a simple model2015

    • Author(s)
      Ryo Akiyama, Takuto Sawayama
    • Organizer
      2015 International Conference of Colloids and Interface Science
    • Place of Presentation
      Taipei
    • Year and Date
      2015-07-21
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Aggregation behavior of macroanions in an electrolyte solution2015

    • Author(s)
      Takuto Sawayama, Ryo Akiyama
    • Organizer
      The 9th Mini Symposium on Liquids
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-07-04
    • Related Report
      2015 Research-status Report
  • [Presentation] Dependence of Effective Potential of Mean Force between Negatively Charged Colloidal Particles Immersed in an Electrolyte Solution on Charge of Small Anion2015

    • Author(s)
      Takumi Yamashita, Ryo Akiyama
    • Organizer
      The 9th Mini Symposium on Liquids
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-07-04
    • Related Report
      2015 Research-status Report
  • [Presentation] Solute Size Dependence of Preferential Interaction in Hard-Sphere Mixture2015

    • Author(s)
      Yuichi Kawabata, Ryo Akiyama
    • Organizer
      The 9th Mini Symposium on Liquids
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-07-04
    • Related Report
      2015 Research-status Report
  • [Presentation] Energy Conversion Efficiency of Solvation Motor driven by a Reaction on the Motor Surface2015

    • Author(s)
      Ken Tokunaga, Ryo Akiyama
    • Organizer
      The 9th Mini Symposium on Liquids
    • Place of Presentation
      Fukuoka
    • Year and Date
      2015-07-04
    • Related Report
      2015 Research-status Report
  • [Book] Theoretical Studies of Strong Attractive Interaction Between Macro-anions Mediated by Multivalent Metal Cations and Related Association Behavior: Effective Interaction Between ATP-Binding Proteins Can Be Regulated by Hydrolysis "The Role of Water in ATP Hydrolysis Energy Transduction by Protein Machinery" (Ed. Makoto Suzuki)2018

    • Author(s)
      Ryo Akiyama
    • Total Pages
      353
    • Publisher
      Springer
    • ISBN
      9789811084591
    • Related Report
      2018 Annual Research Report
  • [Book] 安池智一、秋山良2016

    • Author(s)
      エントロピーからはじめる熱力学
    • Total Pages
      300
    • Publisher
      放送大学教育振興会
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2020-03-30  

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