• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to project page

2021 Fiscal Year Annual Research Report

Exploring a Guideline for Inhibiting the Peptide Aggregation through All-Atom Analysis of Cosolvent Effect

Research Project

Project/Area Number 19H04206
Research InstitutionOsaka University

Principal Investigator

松林 伸幸  大阪大学, 基礎工学研究科, 教授 (20281107)

Project Period (FY) 2019-04-01 – 2022-03-31
Keywords溶媒和 / 凝集 / リガンド結合 / MDシミュレーション / 溶液理論 / 多変量解析 / 共溶媒 / 分子間相互作用
Outline of Annual Research Achievements

本研究の目的は、全原子モデルを用いた分子動力学シミュレーション(MD)とエネルギー表示溶液理論による自由エネルギー計算から、凝集性などタンパク質の相互作用に対する共溶媒添加効果を解析することである。前年度までに、パーキンソン病に関わるNACoreペプチドを対象として、中性およびイオン性の共溶媒がその凝集性に及ぼす効果を解析し、多変量解析に基づいて凝集性の変化につながる相互作用成分を明らかにしてきた。本年度は、解析対象をタンパク質のリガンド結合に拡げた。全原子MDとエネルギー表示溶液理論の融合手法および多変量解析を、前年度までと同様に用いた。共溶媒種は、尿素、エタノール、ポリエチレングリコール(PEG)、ジメチルスルホキシド(DMSO)、および、1,6-ヘキサンジオールである。尿素とエタノールは代謝物であり、PEGは水溶性のクラウダー、DMSOは凍結保護剤、そして、1,6-ヘキサンジオールは相分離阻害剤として利用されている。共溶媒添加による結合自由エネルギーの変化を全原子モデルで計算したところ、尿素、DMSO、または、1,6-ヘキサンジオールを添加すると解離が促進され、エタノールまたはPEGを添加すると結合が促進されることが分かった。尿素とDMSOの結果は、前年度までのNACoreペプチドの凝集に関わる結果とパラレルであり、1,6-ヘキサンジオールやエタノール、PEGについての結果はタンパク質凝集の一般的な傾向と一致している。共溶媒の選択によりリガンド複合体を解離と促進の両方向にシフト可能であることが明らかになった。さらに、共溶媒添加に伴う結合自由エネルギーの変化を、静電成分、分散引力成分、排除体積成分などからの寄与に分割したところ、共溶媒種によらず、静電成分は結合を促進し分散引力成分は解離を促進することが示された。水と比較しての共溶媒種の極性やサイズを反映している。

Research Progress Status

令和3年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和3年度が最終年度であるため、記入しない。

  • Research Products

    (28 results)

All 2022 2021 Other

All Int'l Joint Research (4 results) Journal Article (19 results) (of which Int'l Joint Research: 9 results,  Peer Reviewed: 19 results) Presentation (5 results) (of which Int'l Joint Research: 5 results,  Invited: 5 results)

  • [Int'l Joint Research] テンプル大学(米国)

    • Country Name
      U.S.A.
    • Counterpart Institution
      テンプル大学
  • [Int'l Joint Research] ヨーク大学(英国)

    • Country Name
      UNITED KINGDOM
    • Counterpart Institution
      ヨーク大学
  • [Int'l Joint Research] ルント大学(スウェーデン)

    • Country Name
      SWEDEN
    • Counterpart Institution
      ルント大学
  • [Int'l Joint Research] レーゲンスブルク大学(ドイツ)

    • Country Name
      GERMANY
    • Counterpart Institution
      レーゲンスブルク大学
  • [Journal Article] Ensemble transformation in the fluctuation theory2022

    • Author(s)
      Shimizu Seishi、Matubayasi Nobuyuki
    • Journal Title

      Physica A: Statistical Mechanics and its Applications

      Volume: 585 Pages: 126430~126430

    • DOI

      10.1016/j.physa.2021.126430

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Simulating the nematic-isotropic phase transition of liquid crystal model via generalized replica-exchange method2022

    • Author(s)
      Takemoto Kengo、Ishii Yoshiki、Washizu Hitoshi、Kim Kang、Matubayasi Nobuyuki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 156 Pages: 014901~014901

    • DOI

      10.1063/5.0073105

    • Peer Reviewed
  • [Journal Article] Anion?cation contrast of small molecule solvation in salt solutions2022

    • Author(s)
      Hervoe-Hansen Stefan、Heyda Jan、Lund Mikael、Matubayasi Nobuyuki
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 24 Pages: 3238~3249

    • DOI

      10.1039/d1cp04129k

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)2022

    • Author(s)
      Kikutsuji Takuma、Mori Yusuke、Okazaki Kei-ichi、Mori Toshifumi、Kim Kang、Matubayasi Nobuyuki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 156 Pages: 154108~154108

    • DOI

      10.1063/5.0087310

    • Peer Reviewed
  • [Journal Article] Cooperativity in micellar solubilization2021

    • Author(s)
      Shimizu Seishi、Matubayasi Nobuyuki
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 23 Pages: 8705~8716

    • DOI

      10.1039/d0cp06479c

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Understanding the scaling of boson peak through insensitivity of elastic heterogeneity to bending rigidity in polymer glasses2021

    • Author(s)
      Tomoshige Naoya、Goto Shota、Mizuno Hideyuki、Mori Tatsuya、Kim Kang、Matubayasi Nobuyuki
    • Journal Title

      Journal of Physics: Condensed Matter

      Volume: 33 Pages: 274002~274002

    • DOI

      10.1088/1361-648X/abfd51

    • Peer Reviewed
  • [Journal Article] Transition pathway of hydrogen bond switching in supercooled water analyzed by the Markov state model2021

    • Author(s)
      Kikutsuji Takuma、Kim Kang、Matubayasi Nobuyuki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 154 Pages: 234501~234501

    • DOI

      10.1063/5.0055531

    • Peer Reviewed
  • [Journal Article] Sorption: A Statistical Thermodynamic Fluctuation Theory2021

    • Author(s)
      Shimizu Seishi、Matubayasi Nobuyuki
    • Journal Title

      Langmuir

      Volume: 37 Pages: 7380~7391

    • DOI

      10.1021/acs.langmuir.1c00742

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Adsorbate-adsorbate interactions on microporous materials2021

    • Author(s)
      Shimizu Seishi、Matubayasi Nobuyuki
    • Journal Title

      Microporous and Mesoporous Materials

      Volume: 323 Pages: 111254~111254

    • DOI

      10.1016/j.micromeso.2021.111254

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Construction of isostructural hydrogen-bonded organic frameworks: limitations and possibilities of pore expansion2021

    • Author(s)
      Suzuki Yuto、Guti?rrez Mario、Tanaka Senri、Gomez Eduardo、Tohnai Norimitsu、Yasuda Nobuhiro、Matubayasi Nobuyuki、Douhal Abderrazzak、Hisaki Ichiro
    • Journal Title

      Chemical Science

      Volume: 12 Pages: 9607~9618

    • DOI

      10.1039/d1sc02690a

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal2021

    • Author(s)
      Ishii Yoshiki、Matubayasi Nobuyuki、Watanabe Go、Kato Takashi、Washizu Hitoshi
    • Journal Title

      Science Advances

      Volume: 7 Pages: eabf0669

    • DOI

      10.1126/sciadv.abf0669

    • Peer Reviewed
  • [Journal Article] Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions2021

    • Author(s)
      Kojima Hidekazu、Handa Kazuya、Yamada Kazuo、Matubayasi Nobuyuki
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Pages: 9357~9371

    • DOI

      10.1021/acs.jpcb.1c04818

    • Peer Reviewed
  • [Journal Article] Cooperative Sorption on Porous Materials2021

    • Author(s)
      Shimizu Seishi、Matubayasi Nobuyuki
    • Journal Title

      Langmuir

      Volume: 37 Pages: 10279~10290

    • DOI

      10.1021/acs.langmuir.1c01236

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Breakdown of the Stokes?Einstein relation in supercooled liquids: A cage-jump perspective2021

    • Author(s)
      Pastore Raffaele、Kikutsuji Takuma、Rusciano Francesco、Matubayasi Nobuyuki、Kim Kang、Greco Francesco
    • Journal Title

      The Journal of Chemical Physics

      Volume: 155 Pages: 114503~114503

    • DOI

      10.1063/5.0059622

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Temperature Dependence of Sorption2021

    • Author(s)
      Shimizu Seishi、Matubayasi Nobuyuki
    • Journal Title

      Langmuir

      Volume: 37 Pages: 11008~11017

    • DOI

      10.1021/acs.langmuir.1c01576

    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Effects of chain length on Rouse modes and non-Gaussianity in linear and ring polymer melts2021

    • Author(s)
      Goto Shota、Kim Kang、Matubayasi Nobuyuki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 155 Pages: 124901~124901

    • DOI

      10.1063/5.0061281

    • Peer Reviewed
  • [Journal Article] Crystallization of Polyethylene Brushes and Its Effect on Interactions with Water2021

    • Author(s)
      Yagasaki Takuma、Matubayasi Nobuyuki
    • Journal Title

      Macromolecules

      Volume: 54 Pages: 8303~8313

    • DOI

      10.1021/acs.macromol.1c01145

    • Peer Reviewed
  • [Journal Article] Atomistic description of molecular binding processes based on returning probability theory2021

    • Author(s)
      Kasahara Kento、Masayama Ren、Okita Kazuya、Matubayasi Nobuyuki
    • Journal Title

      The Journal of Chemical Physics

      Volume: 155 Pages: 204503~204503

    • DOI

      10.1063/5.0070308

    • Peer Reviewed
  • [Journal Article] Molecular Structure and Vibrational Spectra of Water Molecules Sorbed in Poly(2-methoxyethylacrylate) Revealed by Molecular Dynamics Simulation2021

    • Author(s)
      Yasoshima Nobuhiro、Ishiyama Tatsuya、Gemmei-Ide Makoto、Matubayasi Nobuyuki
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Pages: 12095~12103

    • DOI

      10.1021/acs.jpcb.1c07342

    • Peer Reviewed
  • [Presentation] Water-Polymer Interactions Analyzed by All-Atom MD Simulations: Fugaku Supercomputer Project toward Materials Design2021

    • Author(s)
      Nobuyuki Matubayasi
    • Organizer
      The International Association for the Properties of Water and Steam 2021 Annual Meeting
    • Int'l Joint Research / Invited
  • [Presentation] All-Atom Analysis of Water-Polymer Interactions: Fugaku Supercomputer Project toward Materials Design2021

    • Author(s)
      Nobuyuki Matubayasi
    • Organizer
      International Virtual Symposium on Chemistry: Chemistry Beyond Borders
    • Int'l Joint Research / Invited
  • [Presentation] Energetics of cosolvent effect on peptide aggregation studied through variational principle2021

    • Author(s)
      Nobuyuki Matubayasi
    • Organizer
      Pacifichem 2021
    • Int'l Joint Research / Invited
  • [Presentation] Chain-increment method for free-energy computation of a polymer with all-atom molecular simulation and a theory of solutions2021

    • Author(s)
      Nobuyuki Matubayasi
    • Organizer
      Pacifichem 2021
    • Int'l Joint Research / Invited
  • [Presentation] All-atom analysis of physisorption on solid-liquid interface with molecular simulation and a theory of solutions2021

    • Author(s)
      Nobuyuki Matubayasi
    • Organizer
      Pacifichem 2021
    • Int'l Joint Research / Invited

URL: 

Published: 2022-12-28  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi