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

Investigating ligand-controlled GPCR activation mechanisms by cutting edge simulation

Research Project

Project/Area Number 19H03191
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43040:Biophysics-related
Research InstitutionTokyo Institute of Technology

Principal Investigator

Kitao Akio  東京工業大学, 生命理工学院, 教授 (30252422)

Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,290,000 (Direct Cost: ¥13,300,000、Indirect Cost: ¥3,990,000)
Fiscal Year 2022: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2021: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2020: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2019: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
KeywordsGPCR / PaCS-MD / キネティックス / 構造変化活性化 / 構造変化 / 活性化
Outline of Research at the Start

リガンドの結合によるGタンパク質共役受容体(GPCR)の活性化からGPCRとの結合により活性化されるGタンパク質が解離するに至るまでのメカニズムを、PaCS-MD/MSMなどの最先端のシミュレーション法で明らかにする。まずリガンドがGPCRへ結合・解離する過程をシミュレーションで可視化・定量化し、次にリガンド結合が誘起するGPCRの構造変化とそのメカニズムを解析し、更にGタンパク質のGPCRへの結合と解離・活性化・GPCRからの解離の過程をシミュレーションで再現する。すべての結果を統合して、活性化のメカニズムを分子レベルで明らかにし、GPCRに共通するシグナル伝達原理の解明を目指す。

Outline of Final Research Achievements

In this study, human A2A adenosine receptor (A2AR), a G protein-coupled receptor activated by adenosine, was elucidated as the research target. We investigated the differences in dynamics upon various ligand binding and developed computational methods to predict binding affinity. We also performed state-of-the-art molecular simulations of the activated state of the A2AR bound by a ligand (NECA) and full G proteins consisting of three subunits (Gs and Go) and were able to determine dynamics differences.

Academic Significance and Societal Importance of the Research Achievements

A2ARにリガンド(NECA)とGタンパク質GsとGoが結合した活性化状態の構造を用いてその状態の立体構造モデルを構築し、構造のダイナミクスにどのような違いがあるか明らかにすることができた。この研究は国際共同研究に進展し、A2ARのリガンド結合部位からGタンパク質へ長距離の情報伝達経路を特定でき、またA2ARには、少なくとも2つの不活性状態と3つの活性状態が同時に存在しており、その共存比率がリガンドの結合やGタンパク質の活性化状態に依存して変化することがわかった。

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (113 results)

All 2023 2022 2021 2020 2019 Other

All Int'l Joint Research (5 results) Journal Article (32 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 29 results,  Open Access: 15 results) Presentation (70 results) (of which Int'l Joint Research: 13 results,  Invited: 17 results) Book (2 results) Remarks (4 results)

  • [Int'l Joint Research] University of Tronto(カナダ)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Toronto(カナダ)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of East Anglia(英国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of California, San Diego(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] University of Toronto(カナダ)

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein2023

    • Author(s)
      Mariko Kojima, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Kunio Hirata, Keitaro Yamashita, Yuki Hishikawa, Akio Kitao, Takafumi Ueno
    • Journal Title

      Biomaterial Science

      Volume: 11 Issue: 4 Pages: 1350-1357

    • DOI

      10.1039/d2bm01759h

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of MotA, a flagellar stator protein, from hyperthermophile2023

    • Author(s)
      Tatsuro Nishikino, Norihiro Takekawa, Duy Phuoc Tran, Jun-ichi Kishikawa, Mika Hirose, Sakura Onoe, Seiji Kojima, Michio Homma, Akio Kitao, Takayuki Kato and Katsumi Imada
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 631 Pages: 78-85

    • DOI

      10.1016/j.bbrc.2022.09.072

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dependence of Vibrational Energy Transfer on Distance in a Four-helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices2022

    • Author(s)
      Satoshi Yamashita,Misao Mizuno, Kazuhiro Takemura, Akio Kitao, and Yasuhisa Mizutani
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: - Issue: 17 Pages: 3283-3290

    • DOI

      10.1021/acs.jpcb.2c00956

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules2022

    • Author(s)
      Akio Kitao
    • Journal Title

      J Multidisciplinary Scientific Journal

      Volume: 5 Issue: 2 Pages: 298-317

    • DOI

      10.3390/j5020021

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Conserved GYXLI Motif of FlhA Is Involved in Dynamic Domain Motions of FlhA Required for Flagellar Protein Export2022

    • Author(s)
      Minamino Tohru、Kinoshita Miki、Inoue Yumi、Kitao Akio、Namba Keiichi
    • Journal Title

      Microbiology Spectrum

      Volume: 10 Issue: 4

    • DOI

      10.1128/spectrum.01110-22

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer2022

    • Author(s)
      Tran Duy Phuoc、Taira Yuta、Ogawa Takumi、Misu Ryoga、Miyazawa Yoshiki、Kitao Akio
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1

    • DOI

      10.1038/s41598-022-07792-2

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM2022

    • Author(s)
      Sobeh Mohamed Marzouk、Kitao Akio
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 62 Issue: 5 Pages: 1294-1307

    • DOI

      10.1021/acs.jcim.1c01508

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL2021

    • Author(s)
      Yamawaki Takeo、Mizuno Misao、Ishikawa Haruto、Takemura Kazuhiro、Kitao Akio、Shiro Yoshitsugu、Mizutani Yasuhisa
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 125 Issue: 25 Pages: 6847-6856

    • DOI

      10.1021/acs.jpcb.1c01885

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides2021

    • Author(s)
      Tran Duy Phuoc、Tada Seiichi、Yumoto Akiko、Kitao Akio、Ito Yoshihiro、Uzawa Takanori、Tsuda Koji
    • Journal Title

      Scientific Reports

      Volume: 11 Issue: 1

    • DOI

      10.1038/s41598-021-90245-z

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The role of the half-turn in determining structures of Alzheimer’s Aβ wild-type and mutants2021

    • Author(s)
      Hayward Steven、Kitao Akio
    • Journal Title

      Journal of Structural Biology

      Volume: 213 Issue: 4 Pages: 107792-107792

    • DOI

      10.1016/j.jsb.2021.107792

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model2021

    • Author(s)
      Hata Hiroaki、Phuoc Tran Duy、Marzouk Sobeh Mohamed、Kitao Akio
    • Journal Title

      Biophysics and Physicobiology

      Volume: 18 Issue: 0 Pages: 305-316

    • DOI

      10.2142/biophysico.bppb-v18.037

    • NAID

      130008132038

    • ISSN
      2189-4779
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling2021

    • Author(s)
      Huang, S. K., Pandey, A., Tran, D. P., Villanueva, N. L., Kitao, A., Sunahara, R. K., Sljoka, A. and Prosser, R. S.
    • Journal Title

      Cell

      Volume: 184 Issue: 7 Pages: 1884-1894.e14

    • DOI

      10.1016/j.cell.2021.02.041

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins2020

    • Author(s)
      Kenichiro Takaba, Duy Phuoc Tran and Akio Kitao
    • Journal Title

      J. Chem. Phys.

      Volume: 152 Issue: 22 Pages: 225101-225101

    • DOI

      10.1063/5.0004654

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Regulation of caveolae through cholesterol-depletion-dependent tubulation mediated by PACSIN22020

    • Author(s)
      Gusmira Aini、Takemura Kazuhiro、Lee Shin Yong、Inaba Takehiko、Hanawa-Suetsugu Kyoko、Oono-Yakura Kayoko、Yasuhara Kazuma、Kitao Akio、Suetsugu Shiro
    • Journal Title

      Journal of Cell Science

      Volume: 133 Pages: 1-11

    • DOI

      10.1242/jcs.246785

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] PaCS-MD/MSM: Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method2020

    • Author(s)
      PT Duy, H Hata, T Ogawa, Y Taira, A Kitao
    • Journal Title

      アンサンブル: 分子シミュレーション研究会会誌

      Volume: 22 Pages: 151-156

    • NAID

      130008031955

    • Related Report
      2020 Annual Research Report
  • [Journal Article] バイオ分野での量子コンピュータへの期待2020

    • Author(s)
      北尾彰朗
    • Journal Title

      現代化学

      Volume: 6 Pages: 50-51

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics2020

    • Author(s)
      Hata Hiroaki、Nishiyama Masayoshi、Kitao Akio
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1864 Issue: 2 Pages: 129395-129395

    • DOI

      10.1016/j.bbagen.2019.07.004

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration2020

    • Author(s)
      Hata H., Nishihara Y., Nishiyama M., Sowa Y., Kawagishi I. & Kitao A.
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 2351-2351

    • DOI

      10.1038/s41598-020-59172-3

    • NAID

      120006811771

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Kinetic Selection and Relaxation of the Intrinsically Disordered Region of a Protein upon Binding2020

    • Author(s)
      Tran Duy Phuoc、Kitao Akio
    • Journal Title

      Journal of Chemical Theory and Computation

      Volume: 16 Issue: 4 Pages: 2835-2845

    • DOI

      10.1021/acs.jctc.9b01203

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Association and Dissociation Mechanisms of Protein Complexes and Complex Structure Prediction2019

    • Author(s)
      竹村 和浩、畑 宏明、北尾 彰朗
    • Journal Title

      Butsuri

      Volume: 74 Issue: 8 Pages: 533-541

    • DOI

      10.11316/butsuri.74.8_533

    • NAID

      130007793043

    • ISSN
      0029-0181, 2423-8872
    • Year and Date
      2019-08-05
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility2019

    • Author(s)
      Matthews Nick、Kitao Akio、Laycock Stephen、Hayward Steven
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 印刷中 Issue: 6 Pages: 2900-2912

    • DOI

      10.1021/acs.jcim.9b00112

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural insights into the substrate specificity switch mechanism of the type III protein export apparatus2019

    • Author(s)
      Y., Y. Ogawa, M. Kinoshita, N. Terahara, M. Shimada, N. Kodera, T. Ando, K. Namba, A. Kitao, K. Imada, T. Minamino
    • Journal Title

      Structure

      Volume: 印刷中 Issue: 6 Pages: 965-976

    • DOI

      10.1016/j.str.2019.03.017

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Universality and Structural Implications of the Boson Peak in Proteins2019

    • Author(s)
      Nakagawa Hiroshi、Joti Yasumasa、Kitao Akio、Yamamuro Osamu、Kataoka Mikio
    • Journal Title

      Biophysical Journal

      Volume: 117 Issue: 2 Pages: 229-238

    • DOI

      10.1016/j.bpj.2019.06.007

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor2019

    • Author(s)
      Y. Onoue, M. Iwaki, A. Shinobu, Y. Nishihara, H. Iwatsuki, H. Terashima, A. Kitao, H. Kandori*, M. Homma*
    • Journal Title

      Sci. Rep.

      Volume: 9 Issue: 1 Pages: 11216-11216

    • DOI

      10.1038/s41598-019-46038-6

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method2019

    • Author(s)
      Shin Kento、Tran Duy Phuoc、Takemura Kazuhiro、Kitao Akio、Terayama Kei、Tsuda Koji
    • Journal Title

      ACS Omega

      Volume: 4 Issue: 9 Pages: 13853-13862

    • DOI

      10.1021/acsomega.9b01480

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra2019

    • Author(s)
      Joti Yasumasa、Kitao Akio
    • Journal Title

      Biophysics and Physicobiology

      Volume: 16 Issue: 0 Pages: 240-247

    • DOI

      10.2142/biophysico.16.0_240

    • NAID

      130007752764

    • ISSN
      2189-4779
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] More efficient screening of protein-protein complex model structures for reducing the number of candidates2019

    • Author(s)
      Takemura Kazuhiro、Kitao Akio
    • Journal Title

      Biophysics and Physicobiology

      Volume: 16 Issue: 0 Pages: 295-303

    • DOI

      10.2142/biophysico.16.0_295

    • NAID

      130007752767

    • ISSN
      2189-4779
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS72019

    • Author(s)
      Hanawa-Suetsugu Kyoko et al.
    • Journal Title

      Nature Communications

      Volume: 10 Issue: 1 Pages: 4763-4763

    • DOI

      10.1038/s41467-019-12738-w

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] evERdock BAI: Machine-learning-guided selection of protein-protein complex structure2019

    • Author(s)
      Terayama Kei、Shinobu Ai、Tsuda Koji、Takemura Kazuhiro、Kitao Akio
    • Journal Title

      The Journal of Chemical Physics

      Volume: 151 Issue: 21

    • DOI

      10.1063/1.5129551

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins2019

    • Author(s)
      Yokochi Yuichi、Sugiura Kazunori、Takemura Kazuhiro、Yoshida Keisuke、Hara Satoshi、Wakabayashi Ken-ichi、Kitao Akio、Hisabori Toru
    • Journal Title

      Journal of Biological Chemistry

      Volume: 294 Issue: 46 Pages: 17437-17450

    • DOI

      10.1074/jbc.ra119.010401

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An Efficient Timer and Sizer of Biomacromolecular Motions2019

    • Author(s)
      Chan Justin、Takemura Kazuhiro、Lin Hong-Rui、Chang Kai-Chun、Chang Yuan-Yu、Joti Yasumasa、Kitao Akio、Yang Lee-Wei
    • Journal Title

      Structure

      Volume: 28 Issue: 2 Pages: 259-269.e8

    • DOI

      10.1016/j.str.2019.10.020

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] I-BARドメインの細胞膜結合と細胞膜変形 (特集 実験と分子シミュレーションのインタープレイ)2019

    • Author(s)
      竹村和浩, 塙(末次) 京子, 末次志郎, 北尾彰朗
    • Journal Title

      アンサンブル : 分子シミュレーション研究会会誌

      Volume: 21 Pages: 204-207

    • Related Report
      2019 Annual Research Report
  • [Presentation] Revealing the complex formation / deformation process of anti-tumor suppressor p53 protein complexes in functioning2023

    • Author(s)
      Duy Phuoc Tran, Akio Kitao
    • Organizer
      APATCC-10(Asia Pacific Conference of Theoretical and Computational Chemistry
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] LPリング中のロッドの回転シミュレーション Simulating the rod rotation in LP-ring2023

    • Author(s)
      北尾彰朗
    • Organizer
      2022年度べん毛研究交流会
    • Related Report
      2022 Annual Research Report
  • [Presentation] イオン透過に関わるMotAとMotBの相対運動 The relative motions of MotA and MotB in flagellar stator toward ion permeation)2023

    • Author(s)
      Duy Phuoc Tran
    • Organizer
      2022年度べん毛研究交流会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 柔らかな分子の複合体形成と解離2022

    • Author(s)
      北尾彰朗
    • Organizer
      シンポジウム「柔らかな分子系研究の発展」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Conformational Change and Dissociation/Association of Biological Macromolecules Investigated by Parallel Cascade Selection Molecular Dynamics and Markov State Model2022

    • Author(s)
      Akio Kitao
    • Organizer
      ABA, APPA&TBS Joint Congress2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] PaCS-MD/MSM法を用いたキナーゼ複合体の結合速度論解析2022

    • Author(s)
      竹村和浩, 北尾彰朗
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Substrate Unbinding Mechanism of Candida rugosa Lipase Explored by Parallel Cascade Selections Molecular Dynamics and Markov State Model2022

    • Author(s)
      Darin Flamandita, Akio Kitao
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] How EGCG pertubates the interaction between MDM2 and N-terminal domain of p532022

    • Author(s)
      Duy Phuoc Tran, Akio Kitao
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Binding Kinetics of Kinase Complexes by PaCS-MD/MSM2022

    • Author(s)
      竹村和浩, 北尾彰朗
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Protein conformational change, association and dissociation observed using Fugaku and massively parallel molecular dynamics simulations2022

    • Author(s)
      Akio Kitao
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 高速分子動画を補完する構造変化の自由エネルギー地形と経路・流量の解析2022

    • Author(s)
      北尾彰朗
    • Organizer
      令和4年度新学術領域研究「高速分子動画」シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] 分子動力学計算におけるタンパク質の二面角遷移の解析2022

    • Author(s)
      吉岡美月, 北尾彰朗
    • Organizer
      第16回分子科学討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 並列カスケード選択分子動力学法を用いた生体分子の解離課程解析2022

    • Author(s)
      中矢光, チャンフズイ, 北尾彰朗
    • Organizer
      第16回分子科学討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Analysis of High Speed Atomic Force Microscopy Image of FlhAc(FlhAcの高速原子間力顕微鏡画像の解析)2022

    • Author(s)
      大沢陸輝, 北尾彰朗
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] The relative motion of MotA around MotB in bacterial flagellar stator2022

    • Author(s)
      Duy Phuoc Tran, Akio Kitao
    • Organizer
      第60回日本生物物理学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] FlhAcの高速原子間力顕微鏡画像の解析2022

    • Author(s)
      大沢陸輝, 寺原直矢, 古寺哲幸, 今田勝巳, 南野徹, 北尾彰朗
    • Organizer
      第36回分子シミュレーション討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] How different glycopeptide affects the binding of glycoprotein B to paired immunoglobulin-like type 2 receptor2022

    • Author(s)
      Ting-Yi Chu, Duy Phuoc Tran, Akio Kitao
    • Organizer
      第36回分子シミュレーション討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 線形応答理論を応用した効率的な分子動 力学シミュレーションに基づく自由エネル ギー解析2022

    • Author(s)
      生澤真司, 北尾彰朗
    • Organizer
      第36回分子シミュレーション討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] How partial agonist ligands induce the conformational changes of Adenosine A2a receptor2022

    • Author(s)
      Duy Phuoc Tran, Akio Kitao
    • Organizer
      第36回分子シミュレーション討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Molecular Dynamics investigation of binding affinities between amino acid and taste receptor2022

    • Author(s)
      Thai-Hao Nguyen, Duy Phuoc Tran, Akio Kitao
    • Organizer
      第36回分子シミュレーション討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] The Effect of Tricaprylin-Water Interface on the Conformational Dynamics of Candida antarctica Lipase B2022

    • Author(s)
      Tegar Wijaya, Akio Kitao
    • Organizer
      第36回分子シミュレーション討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] SARS-CoV-2 エンドリボヌクレアーゼのオリゴマー化阻害2021

    • Author(s)
      北尾彰朗
    • Organizer
      新学術領域「高速分子動画」Web セミナー「構造生物学・化学・計算科学を融合させたウイルス・パンデミックに対する取り組み」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] インシリコシミュレーションで探るタンパク質複合体の結合親和性とキネティックス2021

    • Author(s)
      北尾彰朗
    • Organizer
      日本薬学会構造活性相関部門構造活性フォーラム2021「次期スーパーコンピュータ「富岳」時代の計算創薬」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Simulated dissociation/association dynamics between proteins and other molecules2021

    • Author(s)
      Akio Kitao
    • Organizer
      TSRC WS「Protein Dynamics」
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Observing biomolecules through a lens of computer simulation2021

    • Author(s)
      北尾彰朗, TRAN Phuoc Duy
    • Organizer
      C2C Program Kick off symposium
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] PaCS-MD/MSM to investigate protein motions and association/dissociation of protein complexes2021

    • Author(s)
      Akio Kitao
    • Organizer
      Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Molecular movie of protein association/dissociation dynamics2021

    • Author(s)
      北尾彰朗
    • Organizer
      第59回日本生物物理学会年会シンポジウム(原子レベルの動的構造解析が拓く生体分子機能の理解)
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Roles of hydration/dehydration for dissociation, association and stabilization of protein complexes2021

    • Author(s)
      Akio Kitao
    • Organizer
      Pacific Chem 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Transport mechanisms of ions, peptides and proteins through the biological membrane2021

    • Author(s)
      Akio Kitao
    • Organizer
      Pacific Chem 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Atomic mechanism of the complete association of intrinsically disordered peptide to protein2021

    • Author(s)
      Duy Tran, Akio Kitao
    • Organizer
      XXXII IUPAP Conference on Computational Physics(ccp2021)
    • Related Report
      2021 Annual Research Report
  • [Presentation] 結合速度論解析2021

    • Author(s)
      北尾彰朗
    • Organizer
      「富岳」2021ワークショップ
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Application of ColDock to docking of cryptic pockets2021

    • Author(s)
      Ryunosuke Kiuchi, Kazuhiro Takemura, Akio Kitao
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNA bending enhances the dissociation of tetrameric p53’s coredomains2021

    • Author(s)
      Duy Tran, Akio Kitao
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock2021

    • Author(s)
      Kazuhiro Takemura, Akio Kitao
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Dynamics of Close-Open State of CALB Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model2021

    • Author(s)
      Wijaya Tegar N., 北尾彰朗
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Investigating the dissociation process and kinetic rates of DBD-p53/DNA complex by PaCS-MD and MSM2021

    • Author(s)
      マルゾーク モハメド, 北尾彰朗
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock2021

    • Author(s)
      竹村和浩, 北尾彰朗
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Benchmarking the free energy calculation of PaCS-MD/MSM2021

    • Author(s)
      チャン フ ズイ, 畑 宏明,中矢 光, 北尾彰朗
    • Organizer
      第21回日本蛋白質科学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Predicting the complex conformations of protein/intrinsically disordered peptide complexes using a method termed a/dPaCS-MD2021

    • Author(s)
      Duy Phuoc Tran, Akio Kitao
    • Organizer
      The Protein Society-35th Anniversary Symposium
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Binding free energy calculation with dPaCS-MD/MSM2021

    • Author(s)
      Duy Phuoc Tran, Akio Kitao
    • Organizer
      C2C Program Kick off symposium
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Dynamics of Close-Open State of Candida antarctica Lipase B Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model2021

    • Author(s)
      Wijaya Tegar Nurwahyu、北尾彰朗
    • Organizer
      第10回日本生物物理学会関東支部会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock2020

    • Author(s)
      竹村和浩、北尾彰朗
    • Organizer
      第20回日本蛋白質科学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Simulating the association/dissociation process of flexible protein complexes2020

    • Author(s)
      Tran P. Duy、Akio Kitao
    • Organizer
      第20回日本蛋白質科学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics2020

    • Author(s)
      宮澤佳希、Duy Phuoc Tran、竹村和浩、北尾彰朗
    • Organizer
      第20回日本蛋白質科学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock2020

    • Author(s)
      竹村和浩、北尾彰朗
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] PaCS-MD/MSM を用いたタンパク質複合体の速度定数評価(Kinetic rate evaluation for protein complexes by PaCS-MD/MSM)2020

    • Author(s)
      宮澤佳希、Phuoc Duy Tran、竹村和浩、北尾彰朗
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Investigating the dissociation process of DBD-p53/DNA complex by PaCS-MD and MSM2020

    • Author(s)
      Sobeh Mohamed Marzouk、北尾彰朗
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 分子動力学計算によるp53-C 末端部位のDNA 結合機構の解明(DNA binding mechanisms of the p53 C-terminal domain elucidated by MD simulation)2020

    • Author(s)
      平悠太、Duy Tran、北尾彰朗
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 分子動力学計算によるp53-C 末端部位のDNA 結合機構の解明2020

    • Author(s)
      平悠太、Tran Duy、北尾彰朗
    • Organizer
      第34回分子シミュレーション討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] PaCS-MD/MSM を用いたタンパク質-タンパク質複合体の結合親和性評価2020

    • Author(s)
      宮澤佳希、Tran Phuoc Duy、竹村和浩、北尾彰朗
    • Organizer
      第34回分子シミュレーション討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] PaCS-MDによるアクトミオシンの結合解離予測2020

    • Author(s)
      尾川拓巳、Tran Duy、藤井高志、難波啓一、北尾彰朗
    • Organizer
      第34回分子シミュレーション討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] PaCS-MDによるタンパク質-タンパク質複合体の解離シミュレーション2020

    • Author(s)
      宮澤佳希、Tran Phuoc Duy、竹村和浩、北尾彰朗
    • Organizer
      第9回日本生物物理学会関東支部会
    • Related Report
      2019 Annual Research Report
  • [Presentation] PaCS-MDによるアクトミオシンの結合解離予測2020

    • Author(s)
      尾川拓巳、Tran Phuoc Duy、藤井高志、難波啓一、北尾彰朗
    • Organizer
      第9回日本生物物理学会関東支部会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Association and dissociation mechanisms of proteins and peptides2019

    • Author(s)
      Akio Kitao
    • Organizer
      WRHI国際ワークショップ
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Calculation of binding free energy and kinetic rates with flexible protein docking(フレキシブルドッキングによる結合自由エネルギーと速度定数計算)2019

    • Author(s)
      Tran Duy、北尾彰朗
    • Organizer
      第57日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Simulating Protein Complex Formation and Dissociation2019

    • Author(s)
      北尾彰朗
    • Organizer
      第10回豊田理研国際WS「Science of Life Phenomena Woven by Water and Biomolecules」
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Simulating protein complex formation and dissociation2019

    • Author(s)
      Akio Kitao
    • Organizer
      TSRC workshop on ‘Protein Dynamics’
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 計算から予測するタンパク質複合体2019

    • Author(s)
      北尾彰朗
    • Organizer
      2019年度日本生化学会関東支部例会内シンポジウム「生化学と先端技術」
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 計算で予測するタンパク質複合体立体構造と結合親和性2019

    • Author(s)
      北尾彰朗
    • Organizer
      第7回 生命理工オープンイノベーションハブ(LiHub)フォーラム ―メゾスケール分子と創薬―
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Binding Energy Calculation of Protein-Peptide Complex Using Unbiased MD Simulations and MSM Analysis2019

    • Author(s)
      Hiroaki Hata, Yasutaka Nishihara, Masayoshi Nishiyama, Ikuro Kawagishi, Akio Kitao
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Structural basis of pressure response of a pressure sensitive YFP variant protein(圧力感受性変異YFPの圧力応答の構造基盤)2019

    • Author(s)
      今田勝巳、辻井美香、永江峰幸、畑 宏明、渡邉朋信、西山雅祥、北尾彰朗、渡邉信久
    • Organizer
      第57日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] An efficient screening, an accurate evaluation, and a simple prediction of protein complex structures2019

    • Author(s)
      竹村和浩、北尾彰朗
    • Organizer
      第57日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Pressure effects on protein-protein interactions studied by molecular dynamics simulations2019

    • Author(s)
      畑 宏明、西原泰孝、西山雅祥、川岸郁朗、北尾彰朗
    • Organizer
      第57日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] PaCS-MDによるタンパク質-タンパク質複合体の解離シミュレーション2019

    • Author(s)
      宮澤佳希、Tran Phuoc Duy、竹村和浩、北尾彰朗
    • Organizer
      スーパーコンピュータワークショップ
    • Related Report
      2019 Annual Research Report
  • [Presentation] DNA recognition mechanisms of the p53 C-terminal domain Investigated by MD simulation(分子動力学計算で探るp53のC末端部位のDNA結合機構)2019

    • Author(s)
      平 悠太、Tran Phuoc Duy、Swadling Jacob、北尾彰朗
    • Organizer
      第57日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Protein-protein complexes dissociation simulated by Parallel Cascade Selection Molecular Dynamics(PaCS-MDによるタンパク質-タンパク質複合体の解離シミュレーション2019

    • Author(s)
      宮澤佳希、Tran Phuoc Duy、竹村和浩、北尾彰朗
    • Organizer
      第57日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 深層学習を用いたタンパク質の天然変性領域の予測2019

    • Author(s)
      三栖涼雅、北尾彰朗、Tran Duy
    • Organizer
      4.  三栖涼雅、北尾彰朗、Tran Duy、“深層学習を用いたタンパク質の天然変性領域の予測”, 日本バイオインフォマティクス学会2019年年会・第8回生命医薬情報学連合大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] タンパク質複合体の構造予測と結合・解離過程の解明2019

    • Author(s)
      畑 宏明、北尾彰朗
    • Organizer
      ポスト「京」重点課題1×重点課題2連携シンポジウム
    • Related Report
      2019 Annual Research Report
  • [Presentation] 圧力による蛋白質の水和を利用した細胞機能の制御(Control of cellular functions through pressure-induced hydration of proteins)2019

    • Author(s)
      畑 宏明、西原泰孝、西山雅祥、川岸郁朗、北尾彰朗
    • Organizer
      第59回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] クラスタリングを用いた蛋白質―蛋白質ドッキング複合体候補構造の効率的絞り込み(A clustering approach to reduce the number of protein-protein docking model candidates2019

    • Author(s)
      竹村和浩、北尾彰朗
    • Organizer
      第59回日本蛋白質科学会年会
    • Related Report
      2019 Annual Research Report
  • [Book] Bacterial and Archaeal Motility, Chapter 3 Molecular Simulation to Investigate Open-Close Motion of a Flagellar Export Apparatus Protein FlhAC2023

    • Author(s)
      Akio Kitao
    • Total Pages
      402
    • Publisher
      Springer
    • ISBN
      9781071630600
    • Related Report
      2022 Annual Research Report
  • [Book] PLASMA MEMBRANE SHAPING, Section 5 Chapter 27 Molecular dynamics2022

    • Author(s)
      Kazuhiro Takemura, Akio Kitao
    • Total Pages
      451
    • Publisher
      Academic Press
    • ISBN
      9780323899116
    • Related Report
      2022 Annual Research Report
  • [Remarks] 北尾研ホームページ

    • URL

      http://www.kitao.bio.titech.ac.jp/

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report 2020 Annual Research Report 2019 Annual Research Report
  • [Remarks] 北尾研twitter

    • URL

      https://twitter.com/compprosci

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report 2020 Annual Research Report
  • [Remarks] 北尾研Facebook

    • URL

      https://www.facebook.com/CompProtSci/

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report 2020 Annual Research Report
  • [Remarks] 北尾研YouTube

    • URL

      https://www.youtube.com/channel/UCuUd9AnHzKNHPqRt7PHy99g/videos

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report 2020 Annual Research Report

URL: 

Published: 2019-04-18   Modified: 2024-01-30  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi