論文

• Shinji Ikizawa, Tatsuki Hori, Tegar Nurwahyu Wijaya, Hiroshi Kono, Zhen Bai, Tatsuhiro Kimizono, Wenbo Lu, Duy Phuoc Tran, Akio Kitao. PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses, The Journal of Physical Chemistry B, 128, 15, 3631-3642, Apr. 2024.  公式リンク  
  
• Tegar N. Wijaya, Akio Kitao. Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM, The Journal of Physical Chemistry B, 127, 34, 7431–7441, Aug. 2023.  公式リンク  
  
• Mariko Kojima, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Kunio Hirata, Keitaro Yamashita, Yuki Hishikawa, Akio Kitao, Takafumi Ueno. Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein, Biomater. Sci., vol. 11, no. 4, pp. 1350-1357, Feb. 2023.
• Tatsuro Nishikino, Norihiro Takekawa, Duy Phuoc Tran, Jun-ichi Kishikawa, Mika Hirose, Sakura Onoe, Seiji Kojima, Michio Homma, Akio Kitao, Takayuki Kato, Katsumi Imada. Structure of MotA, a flagellar stator protein, from hyperthermophile, Biochemical and Biophysical Research Communications, Nov. 2022.  公式リンク  
  
• Akio Kitao. Conserved GYXLI Motif of FlhA Is Involved in Dynamic Domain Motions of FlhA Required for Flagellar Protein Export, Microbiology Spectrum, July 2022.  公式リンク  
  
• Satoshi Yamashita, Misao Mizuno, Kazuhiro Takemura, Akio Kitao, Yasuhisa Mizutani. Dependence of Vibrational Energy Transfer on Distance in a Four-Helix Bundle Protein: Equidistant Increments with the Periodicity of α Helices, The Journal of Physical Chemistry B, May 2022.  公式リンク  
  
• Akio Kitao. Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM, Journal of Chemical Information and Modeling, Mar. 2022.  公式リンク  
  
• Duy Phuoc Tran, Yuta Taira, Takumi Ogawa, Ryoga Misu, Yoshiki Miyazawa, Akio Kitao. Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer, Scientific Reports, Mar. 2022.  公式リンク  
  
• Hiroaki Hata, Duy Phuoc Tran, Marzouk, Akio Kitao. Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model, Biophysics and Physicobiology, Dec. 2021.  公式リンク  
  
• Steven Hayward, Akio Kitao. The role of the half-turn in determining structures of Alzheimer’s Aβ wild-type and mutants, Journal of Structural Biology, Vol. 213, No. 4, pp. 107792, Dec. 2021.  公式リンク  
  
• Takeo Yamawaki, Misao Mizuno, Haruto Ishikawa, Kazuhiro Takemura, Akio Kitao, Yoshitsugu Shiro, Yasuhisa Mizutani. Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL, The Journal of Physical Chemistry B, Vol. 125, No. 25, pp. 6847-6856, June 2021.  公式リンク  
  
• Duy Phuoc Tran, Akio Kitao. Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides, Scientific Reports, Vol. 11, No. 1, May 2021.  公式リンク  
  
• Akio Kitao. Delineating the conformational landscape of the adenosine A_2A receptor during G protein coupling., Cell, Mar. 2021.  公式リンク  
  
• Hiroaki Hata, Yasutaka Nishihara, Masayoshi Nishiyama, Yoshiyuki Sowa, Ikuro Kawagishi, Akio Kitao. High pressure inhibits signaling protein binding to the flagellar motor and bacterial chemotaxis through enhanced hydration, Scientific Reports, Vol. 10, No. 1, Dec. 2020.  公式リンク  
  
• Aini Gusmira, Kazuhiro Takemura, Shin Yong Lee, Takehiko Inaba, Kyoko Hanawa-Suetsugu, Kayoko Oono-Yakura, Kazuma Yasuhara, Akio Kitao, Shiro Suetsugu. Regulation of caveolae through cholesterol-depletion-dependent tubulation mediated by PACSIN2, Journal of Cell Science, Oct. 2020.  公式リンク  
  
• Kenichiro Takaba, Duy Phuoc Tran, Akio Kitao. Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins, The Journal of Chemical Physics, June 2020.  公式リンク  
  
• Kei Terayama, Ai Shinobu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao. evERdock BAI: Machine-learning-guided selection of protein-protein complex structure, The Journal of Chemical Physics, 151, 215104, Dec. 2019.  公式リンク  
  
• Kazuhiro Takemura, Akio Kitao. More efficient screening of protein-protein complex model structures for reducing the number of candidates, Biophysics and Physicobiology, 16, 295-303, Nov. 2019.  公式リンク  
  
• Kyoko Hanawa-Suetsugu, Yuzuru Itoh, Maisarah Ab Fatah, Tamako Nishimura, Kazuhiro Takemura, Kohei Takeshita, Satoru Kubota, Naoyuki Miyazaki, Wan Nurul Izzati Wan Mohamad Noor, Takehiko Inaba, Nhung Thi Hong Nguyen, Sayaka Hamada-Nakahara, Kayoko Oono-Yakura, Masashi Tachikawa, Kenji Iwasaki, Daisuke Kohda, Masaki Yamamoto, Akio Kitao, Atsushi Shimada, Shiro Suetsugu. Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7, Nature Communications, 10, 1, 1-13, Nov. 2019.  公式リンク  
  
• Yasumasa Joti, Akio Kitao. Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra, Biophysics and Physicobiology, 16, 240-247, Nov. 2019.  公式リンク  
  
• Yuichi Yokochi, Kazunori Sugiura, Kazuhiro Takemura, Keisuke Yoshida, Satoshi Hara, Ken-ichi Wakabayashi, Akio Kitao, Toru Hisabori. Impact of key residues within chloroplast thioredoxin-f on recognition for reduction and oxidation of target proteins, Journal of Biological Chemistry, 294, 46, 17437-17450, Nov. 2019.  公式リンク  
  
• Justin Chan, Hong-Rui Lin, Kazuhiro Takemura, Kai-Chun Chang, Yuan-Yu Chang, Yasumasa Joti, Akio Kitao, Lee-Wei Yang. An Efficient Timer and Sizer of Biomacromolecular Motions, Structure, Nov. 2019.  公式リンク  
  
• Kento Shin, Duy Phuoc Tran, Kazuhiro Takemura, Akio Kitao, Kei Terayama, Koji Tsuda. Enhancing Biomolecular Sampling with Reinforcement Learning: A Tree Search Molecular Dynamics Simulation Method, ACS Omega, 4, 9, 13853-13862, Aug. 2019.  公式リンク  
  
• Yasuhiro Onoue, Masayo Iwaki, Ai Shinobu, Yasutaka Nishihara, Hiroto Iwatsuki, Hiroyuki Terashima, Akio Kitao, Hideki Kandori, Michio Homma. Essential ion binding residues for Na+ flow in stator complex of the Vibrio flagellar motor, Scientific Reports, 9, 1, 1-16, Aug. 2019.  公式リンク  
  
• Hiroshi Nakagawa, Yasumasa Joti, Akio Kitao, Osamu Yamamuro, Mikio Kataoka. Universality and Structural Implications of the Boson Peak in Proteins, Biophysical Journal, 117, 2, 229-238, July 2019.  公式リンク  
  
• Hiroaki Hata, Masayoshi Nishiyama, Akio Kitao. Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics, Biochimica et Biophysica Acta (BBA) - General Subjects, July 2019.  公式リンク  
  
• Nick Matthews, Akio Kitao, Stephen Laycock, Steven Hayward. Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility, Journal of Chemical Information and Modeling, 59, 6, 2900-2912, June 2019.  公式リンク  
  
• Yumi Inoue, Yuya Ogawa, Miki Kinoshita, Naoya Terahara, Masafumi Shimada, Noriyuki Kodera, Toshio Ando, Keiichi Namba, Akio Kitao, Katsumi Imada, Tohru Minamino. Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus, Structure, 27, 6, 965-976. e6, June 2019.  公式リンク  
  
• Steven Hayward, Akio Kitao. Multi-strand β-sheet of Alzheimer Aβ(1–40) folds to β-strip helix: implication for protofilament formation, Journal of Biomolecular Structure and Dynamics, 37, 8, pp. 2143-2153, May 2019.  公式リンク  
  
• Duy Phuoc Tran, Akio Kitao. Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model, The Journal of Physical Chemistry B, 123, 11, 2469-2478, Mar. 2019.  公式リンク  
  
• Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao. Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations, The Journal of Chemical Physics, 149, 19, 195101, Nov. 2018.  公式リンク  
  
• Hisham M. Dokainish, Akio Kitao. Similarities and Differences between Thymine(6–4)Thymine/Cytosine DNA Lesion Repairs by Photolyases, The Journal of Physical Chemistry B, 122, 36, 8537-8547, Aug. 2018.  公式リンク  
  
• Kazuhiro Takemura, Chika Sato, Akio Kitao. ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation, The Journal of Physical Chemistry B, 122, 29, 7191-7200, July 2018.  公式リンク  
  
• Satoshi Yamashita, Misao Mizuno, Duy Phuoc Tran, Hisham Dokainish, Akio Kitao, Yasuhisa Mizutani. Vibrational Energy Transfer from Heme through Atomic Contacts in Proteins, The Journal of Physical Chemistry B, Vol. 122, No. 22, pp. 5877-5884, June 2018.  公式リンク  
  
• Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao. Binding free energy analysis of protein-protein docking model structures by evERdock, The Journal of Chemical Physics, 148, 10, 105101, Mar. 2018.  公式リンク  
  
• Jacob B. Swadling, Akio Kitao. Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation, Physical Chemistry Chemical Physics, Vol. 20, No. 5, pp. 2990-3001, Feb. 2018.  公式リンク  
  
• Duy Phuoc Tran, Akio Kitao. Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics, Journal of Chemical Theory and Computation, Vol. 14, No. 1, pp. 404-417, Jan. 2018.  公式リンク  
  
• Kazuhiro Takemura, Kyoko Hanawa-Suetsugu, Shiro Suetsugu, Akio Kitao. Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature, Scientific Reports, Dec. 2017.
• Nick Matthews, Robert Easdon, Akio Kitao, Steven Hayward, Stephen Laycock. High quality rendering of protein dynamics in space filling mode, Journal of Molecular Graphics & Modelling, Vol. 78, pp. 158-167, Nov. 2017.  公式リンク  
  
• Hisham M. Dokainish, Daichi Yamada, Tatsuya Iwata, Hideki Kandori, Akio Kitao. Electron Fate and Mutational Robustness in the Mechanism of (6-4)Photolyase-Mediated DNA Repair, ACS Catalysis, pp. 4835-4845, July 2017.
• Akio Kitao, Nishihara, Yasutaka. Structure of the MotA/B Proton Channel., Methods in molecular biology (Clifton, N.J.), Vol. 1593, pp. 133-145, Apr. 2017.  公式リンク  
  
• Akio Kitao, Kazuhiro Takemura. High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments., Current opinion in structural biology, Vol. 42, pp. 50-58, Feb. 2017.  公式リンク  
  
• Otani, Yuko, Watanabe, Satoshi, Ohwada, Tomohiko, Kitao, Akio, Akio Kitao. Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic beta-Proline Oligomers: Length-Dependent Convergence to Organized Structures, Journal of Physical Chemistry B, Vol. 121, No. 1, pp. 100-109, Jan. 2017.  公式リンク  
  
• Taguchi, Junko, Kitao, Akio, Akio Kitao. Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes, Biophysics and Physicobiology, Vol. 13, No. 0, pp. 117-126, Aug. 2016.
• Dokainish, Hisham M., Kitao, Akio, Akio Kitao. Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step, Acs Catalysis, Vol. 6, No. 8, pp. 5500-5507, Aug. 2016.  公式リンク  
  
• Yamada, D., Dokainish, H. M., Iwata, T., Yamamoto, J., Ishikawa, T., Todo, T., Iwai, S., Getzoff, E. D., Kitao, A., Kandori, H., Akio Kitao. Functional Conversion of CPD and (6-4) Photolyases by Mutation, Biochemistry, Vol. 55, No. 30, pp. 4173-4183, July 2016.  公式リンク  
  
• Deguchi, A., Tomita, T., Ohto, U., Kazuhiro Takemura, Akio Kitao, Miyake, K., Akashi-Takamura, S., Maru, Y.. Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment, Oncogene, Vol. 35, No. 11, pp. 1445-1456, 2016.  公式リンク  
  
• Maru, Yoshiro, Tomita, Takeshi, Deguchi, Atsuko, Ieguchi, Katsuaki, Takita, Morichika, Tsukahara, Fujiko, Takemura, Kazuhiro, Kitao, Akio, Gusovsky, Fabian, Akio Kitao. Drug Targeting Based on a New Concept-Targeting Against TLR4 as an Example, Endocrine Metabolic & Immune Disorders-Drug Targets, Vol. 15, No. 2, pp. 83-87, July 2015.  公式リンク  
  
• Hayward, Steven, Kitao, Akio, Akio Kitao. Monte Carlo Sampling with Linear Inverse Kinematics for Simulation of Protein Flexible Regions, Journal of Chemical Theory and Computation, Vol. 11, No. 8, pp. 3895-3905, 2015.  公式リンク  
  
• Nishihara, Yasutaka, Kitao, Akio, Akio Kitao. Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor, Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, No. 25, pp. 7737-7742, 2015.  公式リンク  
  
• Sakai, Taki, Matsumoto, Yotaro, Ishikawa, Minoru, Sugita, Kazuyuki, Hashimoto, Yuichi, Wakai, Nobuhiko, Kitao, Akio, Morishita, Era, Toyoshima, Chikashi, Hayashi, Tomoatsu, Akiyama, Tetsu, Akio Kitao. Design, synthesis and structure-activity relationship studies of novel sirtuin 2 (SIRT2) inhibitors with a benzamide skeleton, Bioorganic & Medicinal Chemistry, Vol. 23, No. 2, pp. 328-339, 2015.  公式リンク  
  
• Harada, Ryuhei, Kitao, Akio, Akio Kitao. Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins, Journal of Chemical Theory and Computation, Vol. 11, No. 11, pp. 5493-5502, 2015.  公式リンク  
  
• Wakai N, Takemura K, Morita T, Kitao A. Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations., Jan. 2014.  公式リンク  
  
• Takahashi, Nobuaki, Hamada-Nakahara, Sayaka, Itoh, Yuzuru, Takemura, Kazuhiro, Shimada, Atsushi, Ueda, Yoshifumi, Kitamata, Manabu, Matsuoka, Rei, Hanawa-Suetsugu, Kyoko, Senju, Yosuke, Mori, Masayuki X., Kiyonaka, Shigeki, Kohda, Daisuke, Kitao, Akio, Mori, Yasuo, Suetsugu, Shiro, Akio Kitao. TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P-2, Nature Communications, Vol. 5, 2014.
• Yang, Lee-Wei, Kitao, Akio, Huang, Bang-Chieh, Go, Nobuhiro, Akio Kitao. Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories, Biophysical Journal, Vol. 107, No. 6, pp. 1415-1425, 2014.
• Yamamori, Yu, Kitao, Akio, Akio Kitao. MuSTAR MD: Multi-scale sampling using temperature accelerated and replica exchange molecular dynamics, Journal of Chemical Physics, Vol. 139, No. 14, 2013.
• Harada, Ryuhei, Kitao, Akio, Akio Kitao. Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway, Journal of Chemical Physics, Vol. 139, No. 3, 2013.
• Omori, S., Kitao, A., Akio Kitao. CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body proteinprotein docking decoys, Proteins-Structure Function and Bioinformatics, Vol. 81, No. 6, pp. 1005-1016, 2013.
• Ishikawa, Takeshi, Burri, Raghunadha Reddy, Kamatari, Yuji O., Sakuraba, Shun, Matubayasi, Nobuyuki, Kitao, Akio, Kuwata, Kazuo, Akio Kitao. A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method, Physical Chemistry Chemical Physics, Vol. 15, No. 10, pp. 3646-3654, 2013.
• Meshcheryakov, Vladimir A., Kitao, Akio, Matsunami, Hideyuki, Samatey, Fadel A., Akio Kitao. Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins, Acta Crystallographica Section D-Biological Crystallography, Vol. 69, pp. 812-820, 2013.
• Takemura K, Guo H, Sakuraba S, Matubayasi N, Kitao A. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation., Dec. 2012.  公式リンク  
  
• Akio Kitao. The fast-folding mechanism of villin headpiece subdomain studied by multiscale distributed computing, Journal of Chemical Theory and Computation, Vol. 8, No. 1, pp. 290-299, 2012.  公式リンク  
  
• Akio Kitao. Water model tuning for improved reproduction of rotational diffusion and NMR spectral density, Journal of Physical Chemistry B, Vol. 116, No. 22, pp. 6279-6287, 2012.  公式リンク  
  
• Akio Kitao. Erratum: Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding (Journal of Chemical Physics (2011) 135 (045101)), Journal of Chemical Physics, Vol. 135, No. 11, 2011.  公式リンク  
  
• Akio Kitao. Transform and relax sampling for highly anisotropic systems: Application to protein domain motion and folding, Journal of Chemical Physics, Vol. 135, No. 4, 2011.  公式リンク  
  
• Akio Kitao. Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing, Journal of the American Chemical Society, Vol. 133, No. 34, pp. 13571-13576, 2011.  公式リンク  
  
• Akio Kitao. Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models, Chemical Physics Letters, Vol. 503, No. 1-3, pp. 145-152, 2011.  公式リンク  
  
• Akio Kitao. Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method, Journal of Physical Chemistry B, Vol. 115, No. 27, pp. 8806-8812, 2011.  公式リンク  
  
• Akio Kitao. Erratum: Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models (Chemical Physics Letters (2011) 503 (145-152)), Chemical Physics Letters, Vol. 516, No. 1-3, 2011.  公式リンク  
  
• Akio Kitao. Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding, Journal of Structural Biology, Vol. 173, No. 1, pp. 20-28, 2011.  公式リンク  
  
• Akio Kitao. Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export, Molecular Microbiology, Vol. 76, No. 1, pp. 260-268, 2010.  公式リンク  
  
• Akio Kitao. The effect of end constraints on protein loop kinematics, Biophysical Journal, Vol. 98, No. 9, pp. 1976-1985, 2010.  公式リンク  
  
• Akio Kitao. Detecting coupled collective motions in protein by independent subspace analysis, Journal of Chemical Physics, Vol. 133, No. 18, 2010.  公式リンク  
  
• Akio Kitao. Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation, Journal of Molecular Graphics and Modelling, Vol. 28, No. 6, pp. 548-554, 2010.  公式リンク  
  
• Akio Kitao. Erratum: Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): Insights into functional dynamics (Bioinformatics (2009) vol. 25 (5) (606-614)), Bioinformatics, Vol. 25, No. 16, 2009.  公式リンク  
  
• Akio Kitao. DTA: Dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins, Bioinformatics, Vol. 25, No. 5, pp. 628-635, 2009.  公式リンク  
  
• Akio Kitao. Collective dynamics of periplasmic glutamine binding protein upon domain closure, Biophysical Journal, Vol. 97, No. 9, pp. 2541-2549, 2009.  公式リンク  
  
• Akio Kitao. Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): Insights into functional dynamics, Bioinformatics, Vol. 25, No. 5, pp. 606-614, 2009.  公式リンク  
  
• Akio Kitao. Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations, Journal of Computational Chemistry, Vol. 30, No. 12, pp. 1850-1858, 2009.  公式リンク  
  
• Akio Kitao. Hydration affects both harmonic and anharmonic nature of protein dynamics, Biophysical Journal, Vol. 95, No. 6, pp. 2916-2923, 2008.  公式リンク  
  
• Akio Kitao. Thermal unfolding simulations of bacterial flagellin: Insight into its refolding before assembly, Biophysical Journal, Vol. 94, No. 10, pp. 3858-3871, 2008.  公式リンク  
  
• Akio Kitao. Hydration-dependent protein dynamics revealed by molecular dynamics simulation of crystalline staphylococcal nuclease, Journal of Physical Chemistry B, Vol. 112, No. 11, pp. 3522-3528, 2008.  公式リンク  
  
• Akio Kitao. Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra, Biophysical Journal, Vol. 94, No. 11, pp. 4435-4443, 2008.  公式リンク  
  
• Tadaomi Furuta, Fadel A. Samatey, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba, Akio Kitao. Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint, J. Struct. Biol., Vol. 157, No. 3, pp. 481-490, Mar. 2007.  公式リンク  
  
• Akio Kitao. Effects of water model and simulation box size on protein diffusions motions, Journal of Physical Chemistry B, Vol. 111, No. 41, pp. 11870-11872, 2007.  公式リンク  
  
• Akio Kitao. Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation, Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 44, pp. 17261-17265, 2007.  公式リンク  
  
• Akio Kitao. Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation, Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, Vol. 75, No. 4, 2007.  公式リンク  
  
• Akio Kitao. Switch interactions control energy frustration and multiple flagellar filament structures, Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 13, pp. 4894-4899, 2006.  公式リンク  
  
• Akio Kitao. Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase, Biophysical Journal, Vol. 91, No. 5, pp. 1823-1831, 2006.  公式リンク  
  
• Akio Kitao. Protein energy landscape and dynamics studied by molecular simulations and neutron scattering, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme., Vol. 51, No. 8, pp. 972-978, 2006.  公式リンク  
  
• Akio Kitao. Hydration-coupled protein boson peak measured by incoherent neutron scattering, Physica B: Condensed Matter, Vol. 385-386, pp. 871-873, 2006.  公式リンク  
  
• Akio Kitao. Dynamical heterogeneity of protein dynamics studied by elastic incoherent neutron scattering and molecular simulations, Materials Science and Engineering A, Vol. 442, No. 1-2 SPEC. ISS., pp. 356-360, 2006.  公式リンク  
  
• Akio Kitao. Amplitudes and directions of internal protein motions from a JAM analysis of 15N relaxation data, Magnetic Resonance in Chemistry, Vol. 44, No. 7 SPEC. ISS., 2006.  公式リンク  
  
• Akio Kitao. Universal joint of biological supramolecule: mechanism of bacterial flagellar hook investigated in silico, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, Vol. 50, No. 10 Suppl, pp. 1335-1340, 2005.  公式リンク  
  
• Akio Kitao. Protein boson peak originated from hydration-related multiple minima energy landscape, Journal of the American Chemical Society, Vol. 127, No. 24, pp. 8705-8709, 2005.  公式リンク  
  
• Akio Kitao. Structure, function and self-assembly of the bacterial flagellum, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, Vol. 50, No. 10 Suppl, pp. 1328-1334, 2005.  公式リンク  
  
• Akio Kitao. Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism, Nature, Vol. 431, No. 7012, pp. 1062-1068, 2004.  公式リンク  
  
• Akio Kitao. Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering, Physica B: Condensed Matter, Vol. 350, No. 1-3 SUPPL. 1, 2004.  公式リンク  
  
• Akio Kitao. How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme, Protein Engineering, Vol. 16, No. 9, pp. 665-671, 2003.  公式リンク  
  
• Akio Kitao. The Effects of Solvent and Anharmonicity on Incoherent Inelastic Neutron Scattering Spectra of Proteins, Jan. 2002.
• Akio Kitao. Multidimensional replica-exchange method for free-energy calculations, 2000.
• Akio Kitao. A Novel Method to Investigate Functionally-relevant Protein Dynamics., 2000.
• Akio Kitao. A space-time structure determination of human CD2 reveals the CD58-binding mode, Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 5, pp. 2064-2068, 2000.  公式リンク  
  
• Akio Kitao. Molecular dynamics simulation shows large volume fluctuations of proteins, European Biophysics Journal, Vol. 29, No. 7, pp. 472-480, 2000.  公式リンク  
  
• Akio Kitao. Investigating protein dynamics in collective coordinate space, Current Opinion in Structural Biology, Vol. 9, No. 2, pp. 164-169, 1999.  公式リンク  
  
• Akio Kitao. Computational analysis of thermal stability: effect of Ile→Val mutations in human lysozyme, June 1998.
• Akio Kitao. Protein electron transfer reorganization energy spectrum from normal mode analysis. 1. Theory, Journal of Physical Chemistry B, Vol. 102, No. 11, pp. 2076-2084, 1998.  公式リンク  
  
• Akio Kitao. Protein electron transfer reorganization energy spectrum from normal mode analysis. 2. Application to ru-modified cytochrome c, Journal of Physical Chemistry B, Vol. 102, No. 11, pp. 2085-2094, 1998.  公式リンク  
  
• Akio Kitao. Energy landscape of a native protein: Jumping-among-minima model, Proteins: Structure, Function and Genetics, Vol. 33, No. 4, pp. 496-517, 1998.  公式リンク  
  
• Akio Kitao. Dependence of protein stability on the structure of the denatured state: Free energy calculations of 156V mutation in human lysozyme, Biophysical Journal, Vol. 75, No. 5, pp. 2178-2187, 1998.  公式リンク  
  
• Akio Kitao. Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A, Proteins: Structure, Function and Genetics, Vol. 30, No. 4, pp. 388-400, 1998.  公式リンク  
  
• Akio Kitao. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme, Proteins: Structure, Function and Genetics, Vol. 27, No. 3, pp. 425-437, 1997.  公式リンク  
  
• Akio Kitao. Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis, Proteins: Structure, Function and Genetics, Vol. 23, No. 2, pp. 177-186, 1995.  公式リンク  
  
• Akio Kitao. Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis, Protein Science, Vol. 3, No. 6, pp. 936-943, 1994.  公式リンク  
  
• Akio Kitao. A collective motion description of the 310-/α-helix transition: Implications for a natural reaction coordinate, Journal of the American Chemical Society, Vol. 116, No. 14, pp. 6307-6315, 1994.  公式リンク  
  
• Akio Kitao. Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space, Biophysical Chemistry, Vol. 52, No. 2, pp. 107-114, 1994.  公式リンク  
  
• Akio Kitao. Effect of solvent on collective motions in globular protein, Journal of Molecular Biology, Vol. 234, No. 4, pp. 1207-1217, 1993.  公式リンク  
  
• Akio Kitao. Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM theory, Journal of Physical Chemistry, Vol. 97, No. 39, pp. 10231-10235, 1993.  公式リンク  
  
• Akio Kitao. Effects of solvent on the conformation and the collective motions of a protein. 2. Structure of hydration in melittin, Journal of Physical Chemistry, Vol. 97, No. 39, pp. 10223-10230, 1993.  公式リンク  
  
• Akio Kitao. The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum, Chemical Physics, Vol. 158, No. 2-3, pp. 447-472, 1991.  公式リンク  
  
• Kitao, A., Go, N., Akio Kitao. CONFORMATIONAL DYNAMICS OF POLYPEPTIDES AND PROTEINS IN THE DIHEDRAL ANGLE SPACE AND IN THE CARTESIAN COORDINATE SPACE - NORMAL MODE ANALYSIS OF DECA-ALANINE, Journal of Computational Chemistry, Vol. 12, No. 3, pp. 359-368, 1991.  公式リンク  
  

著書

• Akio Kitao. Molecular Simulation to Investigate Open–Close Motion of a Flagellar Export Apparatus Protein FlhAC, Methods in Molecular Biology, pp. 27-34, Feb. 2023.  公式リンク  
• Kazuhiro Takemura, Akio Kitao. Molecular dynamics, Plasma Membrane Shaping, pp. 431-443, Sept. 2022.  公式リンク  

国際会議発表 (査読なし・不明)

• Akio Kitao. Conformational Dynamics and Association/Dissociation Processes of Biological Macromolecules Investigated by Advanced Molecular Simulation, ICMS2023, Oct. 2024.
• Kazuhiro Takemura, Akio Kitao. An efficient screening, an accurate evaluation, and a simple prediction of protein complex structures, Oct. 2024.
• Akio Kitao. Mechanisms of Bacterial flagellar rotation and roles of water as lubricant, Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems, Aug. 2024.
• Akio Kitao. Conformational Change and Association/Dissociation of Proteins investigated by Parallel Cascade Selection Molecular Dynamics, Core-to-core international symposium, Oct. 2023.
• Duy Phuoc Tran, Akio Kitao. Sampling the conformational transition of the monomer of Nsp15 of the SARS-nCoV2 gives a hint to inhibit its hexamer, NanoBioCoM2023, Sept. 2023.
• Duy Phuoc Tran, Akio Kitao. How the bacterial Flagellar Motor stator works: an insight from molecular dynamics simulation, Aug. 2023.
• Akio Kitao. Rotational mechanisms of bacterial flagellumand roles of water, TSRC Workshop on Protein Dynamics, July 2023.
• 北尾彰朗. Conformational Change and Dissociation/Association of Biological Macromolecules Investigated by Parallel Cascade Selection Molecular Dynamics and Markov State Model, ABA, APPA &TBS Joint Congress, June 2023.
• Akio Kitao. Transport mechanisms of ions, peptides and proteins through the biological membrane, Pacific Basin Societies 2021, Dec. 2021.
• Akio Kitao. Roles of hydration/dehydration for dissociation, association and stabilization of protein complexes, Pacific Basin Societies 2021, Dec. 2021.
• Akio Kitao. PaCS-MD/MSM to investigate protein motions and association/dissociation of protein complexes, Symposium on Computer Simulations and Cryo-ET/EM of Complex Biomolecular Systems, Nov. 2021.
• Duy Phuoc Tran, Akio Kitao. Atomic mechanism of the complete association of intrinsically disordered peptide to protein, XXXII IUPAP Conference on Computational Physics(CCP2021), Aug. 2021.
• Akio Kitao. Simulated dissociation/association dynamics between proteins and other molecules, Telluride Science Research Center Workshop on Protein Dynamics, July 2021.
• Duy Tran, Akio Kitao. Predicting the complex conformations of protein/intrinsically disordered peptide complexes, The Protein Society-35th Anniversary Symposium, July 2021.
• Mizuki Tabata, Hisham Dokainish, Keisuke Yamaguchi, Akio Kitao, Shun-ichi Ishiuchi, Masaaki Fujii. GAS PHASE SPECTROSCOPY ON HYDRATED CLUSTERS OF OXYTOCIN BY ELECTROSPRAY IONIZATION / COLD ION TRAP TECHNIQUE, International Symposium on Molecular Spectroscopy, June 2018.

国内会議発表 (査読なし・不明)

• Akio Kitao. Molecular mechanisms of structure support and smooth rotation in the bushing/rod complex of bacterial flagella, 高速分子動画 国際シンポジウム2023, Nov. 2024.
• Duy Phuoc Tran, Kitao Akio. Unveiling the mGLU1 dimer dynamics during partially-active to inactive state transition, 高速分子動画 国際シンポジウム2023, Nov. 2024.
• 北尾彰朗. LPリング内のロッドの回転シミュレーション, 2023年度べん毛研究交流会, Mar. 2024.
• 萩本紗理, 北尾彰朗. Gタンパク質アデノシンA2a受容体複合体活性化ダイナミクスの解明, 第13回日本生物物理学会関東支部会, Mar. 2024.
• 北尾彰朗, 山口智子, 牧野文信, 宮田知子, 南野徹, 加藤貴之, 難波啓一. べん毛LPリング・ロッド系の回転シミュレーション, 生体運動研究合同班会議2024, Jan. 2024.
• Tegar Nurwahyu Wijaya, Akio Kitao. The Effect of Tricaprylin Surface on The Lid Region Dynamics of Candida antarctica Lipase B, Annual Meeting of Biophysical Society of Japan, Nov. 2023.
• Duy Phuoc Tran, Sari Hagimoto, Akio Kitao. Unveiling the dynamics of Adenosine A2a receptor coupling to the G proteins: a molecular dynamics simulation study, Annual Meeting of Biophysical Society of Japan, Nov. 2023.
• 北尾彰朗. タンパク質で構築された軸と軸受け：ロッドとLPリングが働く仕組み, 山田科学振興財団2023年度研究交歓会, Oct. 2023.
• Duy Phuoc Tran, Akio Kitao. Revealing the functional roles of the complex formation/deformation of tumor suppressor p53 protein, The Tenth Project Report Meeting of the HPCI System Including Fugaku, Oct. 2023.
• Duy Phuoc Tran, Akio Kitao. Revealing the complex formation/deformation process of antitumor suppressor p53 protein complexes in functioning, 10TH ASIA-PACIFIC ASSOCIATION OF THEORETICAL AND COMPUTATIONAL CHEMISTRY CONFERENCE (APATCC), Feb. 2023.
• 中矢光, TranPhuoc Duy, 北尾彰朗. 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過程解析, 第16回分子科学討論会, Sept. 2022.
• Darin Flamandita, Akio Kitao. Substrate Unbinding Pathways from Candida rugosa Lipase Investigated by Parallel Cascade Selections Molecular Dynamics and the Markov State Model, 第11回日本生物物理学会関東支部会, Mar. 2022.
• Mariko Kojima, Yuki Hishikawa, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Akio Kitao, Takafumi Ueno. Dynamics structural analysis of miniprotein by in-cell crystal engineering, The 102nd CSJ Annual Meeting (2022), Mar. 2022.
• Akio Kitao. Molecular movie of protein association/dissociation dynamics, 59th Annual Meeting of Biophysical Society of Japan, Nov. 2021.
• Kazuhiro Takemura, Akio Kitao. Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock, 59th Annual Meeting of Biophysical Society of Japan, Nov. 2021.
• Duy Tran, Akio Kitao. DNA bending enhances the dissociation of tetrameric p53’s coredomains, 59th Annual Meeting of Biophysical Society of Japan, Nov. 2021.
• Ryunosuke Kiuchi, Kazuhiro Takemura, Akio Kitao. Application of ColDock to docking of cryptic pockets, 59th Annual Meeting of Biophysical Society of Japan, Nov. 2021.
• Duy Phuoc Tran, Akio Kitao. Binding free energy calculation with dPaCS-MD/MSM, C2C Program Kick off symposium, Oct. 2021.
• 宮澤 佳希, Tran Phuoc Duy, 竹村 和浩, 北尾 彰朗. Parallel Cascade Selection Molecular Dynamics/Markov State Model によるタンパク質－タンパク質複合体の結合親和性評価 (Evaluation of binding affinity for protein-protein complexes by Parallel Cascade Selection Molecular Dynamics/Markov State Model, 第21回日本蛋白質科学会年会, June 2021.
• チャン フ ズイ, 畑 宏明, 中矢 光, 北尾彰朗. Benchmarking the free energy calculation of PaCS-MD/MSM, 第21回日本蛋白質科学会年会, June 2021.
• 竹村 和浩, 北尾 彰朗. PPI-ColDock 法を用いた蛋白質‐ 蛋白質複合体形成, 第21回日本蛋白質科学会年会, June 2021.
• Marzouk, Akio Kitao. Investigating the dissociation process and kinetic rates of DBD-p53/DNA complex by PaCS-MD and MSM, 第21回日本蛋白質科学会年会, June 2021.
• Wijaya Tegar N., 北尾彰朗. Dynamics of Close-Open State of CALB Obtained by Parallel Cascade Molecular Dynamics Simulation and The 2.Wijaya Tegar N.、北尾彰朗「Dynamics of Close-Open State of CALB Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model, 第21回日本蛋白質科学会年会, June 2021.
• 北尾彰朗. 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, 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」, June 2021.
• 北尾彰朗. SARS-CoV-2 エンドリボヌクレアーゼのオリゴマー化阻害, Apr. 2021.
• Mariko Kojima, Yuki Hishikawa, Satoshi Abe, Tadaomi Furuta, Duy Phuoc Tran, Akio Kitao, Takafumi Ueno. Energy Analysis of Miniprotein by in Vivo Protein Crystallization, 日本化学会第101春季年会, Mar. 2021.
• Tegar Nurwahyu Wijaya, Akio Kitao. Dynamics of Close-Open State of Candida antarctica Lipase B Obtained by Parallel Cascade Molecular Dynamics Simulation and The Markov State Model, 第10回日本生物物理学会関東支部会, Mar. 2021.
• 尾川拓巳, TranPhuoc Duy, 藤井 高志, 難波 啓一, 北尾彰朗. PaCS-MDによるアクトミオシンの結合解離予測, 第34回分子シミュレーション討論会 オンライン学会, Dec. 2020.
• 宮澤佳希, TranPhuoc Duy, 竹村和浩, 北尾彰朗. 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, 第34回分子シミュレーション討論会, Dec. 2020.
• 平悠太, TranPhuoc Duy, 北尾彰朗. 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, 第34回分子シミュレーション討論会, Dec. 2020.
• 平悠太, TranPhuoc Duy, 北尾彰朗. 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, Sept. 2020.
• Marzouk, Akio Kitao. Investigating the dissociation process of DBD-p53/DNA complex by PaCS-MD and MSM, Sept. 2020.
• 宮澤佳希, TranPhuoc Duy, 竹村和浩, 北尾彰朗. PaCS-MD/MSM を用いたタンパク質複合体の速度定数評価, Sept. 2020.
• Kazuhiro Takemura, Akio Kitao. Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock, Sept. 2020.
• 北尾彰朗. 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, 第二回新学術「高速分子動画」オンラインセミナー, Aug. 2020.
• 北尾彰朗. SARS-CoV-2タンパク質のオリゴマー化を阻害する薬剤候補分子の探索, Aug. 2020.
• Yoshiki Miyazawa, Duy Phuoc Tran, Kazuhiro Takemura, Akio Kitao. Protein-protein complex dissociation simulated by Parallel Cascade Selection Molecular Dynamics, 第20回日本蛋白質科学会年会, July 2020.
• Duy Phuoc Tran, Akio Kitao. Simulating the association/dissociation process of flexible protein complexes, 第20回日本蛋白質科学会年会, July 2020.
• Kazuhiro Takemura, Akio Kitao. Unguided Binding MD of Protein-Protein Complexes by PPI-ColDock, 第20回日本蛋白質科学会年会, July 2020.
• 北尾彰朗. 長時間ダイナミクス法と 標的分子ネットワーク, Feb. 2020.

その他の論文・著書など

• 畑 宏明, 北尾 彰朗. 高圧力による細菌べん毛モーターの回転制御, 高圧力の科学と技術, 33, 2, 6-75, June 2023.
• Akio Kitao. Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules, J, June 2022.  公式リンク  
  
• Duy Phuoc Tran, Akio Kitao. Calculation of Binding Free Energy and Kinetic Rates with Flexible Protein Docking, Seibutsu Butsuri, Vol. 61, No. 6, pp. 398-399, Nov. 2021.  公式リンク  
  
• 北尾 彰朗. 東京工業大学生命理工学院 北尾研究室, アンサンブル, 分子シミュレーション学会, Vol. 23, No. 1, pp. 67-71, Jan. 2021.
• 北尾 彰朗. バイオ分野での量子コンピュータへの期待, 現代化学, Vol. 6, pp. 50-51, June 2020.
• 北尾彰朗. バイオ分野での量子コンピュータへの期待, 現代化学、v6(No.591)、p50-51, Vol. 6, No. 591, p. 50-51, June 2020.
• Duy Phuoc Tran, Hiroaki Hata, Takumi Ogawa, Yuta Taira, Akio Kitao. PaCS-MD/MSM: Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method, 分子シミュレーション学会誌アンサンブル, Vol. 22, 151-156, Apr. 2020.
• Tran Duy Phuoc, Hata Hiroaki, Ogawa Takumi, Taira Yuta, Kitao Akio, 北尾彰朗. 最近の研究から PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method, アンサンブル, 分子シミュレーション学会, Vol. 22, No. 2, pp. 151-156, Mar. 2020.
• Tran Duy Phuoc, Hata Hiroaki, Ogawa Takumi, Taira Yuta, Kitao Akio, 北尾彰朗. 最近の研究から PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method, アンサンブル, 分子シミュレーション学会, Vol. 22, No. 2, pp. 151-156, Mar. 2020.
• 竹村 和浩, 畑 宏明, 北尾 彰朗. タンパク質複合体構造の形成・解離メカニズムと予測, 日本物理学会誌, 一般社団法人 日本物理学会, Vol. 74, No. 8, pp. 533-541, July 2019.
• Akio Kitao, Hiroaki Hata. Molecular dynamics simulation of bacterial flagella, Biophysical Reviews, 10, 2, 617-629, Apr. 2018.  公式リンク  
  

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