Publications

2024

• Tingting Wang, Takahisa Yamato, Wataru Sugiura

  "Thermal Energy Transport through Nonbonded Native Contacts in Protein"

  2024/08/28, The Journal of Physical Chemistry B

  DOI: 10.1021/acs.jpcb.4c03475

2023

• Tingting Wang, Takahisa Yamato, Wataru Sugiura

  "Site-selective heat current analysis of α-helical protein with linear-homopolymer-like model"

  2023/06/07, The Journal of Chemical Physics

  DOI: 10.1063/5.0149362

2022

• Takahisa Yamato, Tingting Wang, Wataru Sugiura, Olivier Laprévote, Takahiro Katagiri

  "Computational Study on the Thermal Conductivity of a Protein"

  2022/04/28, The Journal of Physical Chemistry B

  DOI: 10.1021/acs.jpcb.2c00958

2020

• Humanath Poudel, Korey M. Reid, Takahisa Yamato, David M. Leitner

  "Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations"

  2020/11/05, The Journal of Physical Chemistry B

  DOI: 10.1021/acs.jpcb.0c08091

• Takahisa Yamato, David M. Leitner

  "Structure, dynamics, and energy flow that govern Heme protein functions: theory and experiments. Session 3SBA at the 57th BSJ Annual Meeting"

  2020/04/30, Biophysical Reviews

  DOI: 10.1007/s12551-020-00625-4

• David M. Leitner, Takahisa Yamato

  "Recent developments in the computational study of protein structural and vibrational energy dynamics"

  2020/04, Biophysical Reviews

  DOI: 10.1007/s12551-020-00661-0

• Korey M. Reid, Takahisa Yamato, David M. Leitner

  "Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin"

  2020/02/20, The Journal of Physical Chemistry B

  DOI: 10.1021/acs.jpcb.9b11413

2019

• Kunitaka Ota, Takahisa Yamato

  "Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein"

  2019/01/31, The Journal of Physical Chemistry B

  DOI: 10.1021/acs.jpcb.8b10489

• Takahisa Yamato, Olivier Laprévote

  "Normal mode analysis and beyond"

  2019, Biophysics and Physicobiology

  DOI: 10.2142/biophysico.16.0_322

2018

• Tatsuya Yamada, Shigeki Mitaku, Takahisa Yamato

  "Characterization of mechanical unfolding intermediates of membrane proteins by coarse grained molecular dynamics simulation"

  2018, Chemical Physics Letters

  DOI: 10.1016/j.cplett.2017.11.025

• Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando, Takahisa Yamato

  "Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited"

  2018, The Journal of Physical Chemistry B

  DOI: 10.1021/acs.jpcb.8b04333

• David M. Leitner, Takahisa Yamato

  "Mapping energy transport networks in proteins"

  2018, arXiv preprint arXiv:1805.03715

  DOI: 10.1002/9781119518068.ch2

• Korey M. Reid, Takahisa Yamato, David M. Leitner

  "Scaling of Rates of Vibrational Energy Transfer in Proteins with Equilibrium Dynamics and Entropy"

  2018, The Journal of Physical Chemistry B

  DOI: 10.1021/acs.jpcb.8b07552

2016

• Tatsuya Yamada, Takahisa Yamato, Shigeki Mitaku

  "Forced unfolding mechanism of bacteriorhodopsin as revealed by coarse-grained molecular dynamics"

  2016, Biophysical journal

  DOI: 10.1016/j.bpj.2016.09.051

2015

• Ryuma Sato, Hirotaka Kitoh-Nishioka, Koji Ando, Takahisa Yamato

  "Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors"

  2015, Chemical Physics Letters

  DOI: 10.1016/j.cplett.2015.05.066

• Takakazu Ishikura, Yuki Iwata, Tatsuro Hatano, Takahisa Yamato

  "Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study"

  2015, Journal of computational chemistry

  DOI: 10.1002/jcc.23989

2014

• Takakazu Ishikura, Tatsuro Hatano, Takahisa Yamato

  "Atomic stress tensor analysis of proteins (vol 539, pg 144, 2012)"

  2014, Chemical Physics Letters

  DOI: 10.1016/j.cplett.2014.07.059

2013

• No Data

  "Combinatorial approach of molecular dynamics simulations and database analyses for the studies of protein structure and function"

  2013, Seikagaku. The Journal of Japanese Biochemical Society

  DOI: nan

2012

• Takakazu Ishikura, Tatsuro Hatano, Takahisa Yamato

  "Atomic stress tensor analysis of proteins"

  2012, Chemical Physics Letters

  DOI: 10.1016/j.cplett.2012.05.005

• Shigefumi Mimura, Takahisa Yamato, Tadashi Kamiyama, Kunihiko Gekko

  "Nonneutral evolution of volume fluctuations in lysozymes revealed by normal-mode analysis of compressibility"

  2012, Biophysical chemistry

  DOI: 10.1016/j.bpc.2011.11.005

2010

• Hiroshi C. Watanabe, Yoshiharu Mori, Takashi Tada, Shozo Yokoyama, Takahisa Yamato

  "Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin"

  2010, Biophysics

  DOI: 10.2142/biophysics.6.67

• Takahisa YAMATO

  "Proteins at Work: Computational Biopolymer Science of Energy, Electron, Proton Transfer and Ligand Migration"

  2010, Kobunshi Ronbunshu

  DOI: 10.1295/koron.67.179

2009

• Hiroshi C. Watanabe, Takakazu Ishikura, Takahisa Yamato

  "Theoretical modeling of the O-intermediate structure of bacteriorhodopsin"

  2009, Proteins: Structure, Function, and Bioinformatics

  DOI: 10.1002/prot.22221

• Ayana Tomita, Tokushi Sato, Kouhei Ichiyanagi, Shunsuke Nozawa, Hirohiko Ichikawa, Matthieu Chollet, Fumihiro Kawai, Sam-Yong Park, Takayuki Tsuduki, Takahisa Yamato, Shin-ya Koshihara, Shin-ichi Adachi

  "Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin"

  2009, Proceedings of the National Academy of Sciences

  DOI: 10.1073/pnas.0807774106

2008

• Yuji Miyazawa, Hirotaka Nishioka, Kei Yura, Takahisa Yamato

  "Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue"

  2008, Biophysical journal

  DOI: 10.1529/biophysj.107.119248

• Kana Koike, Kazutomo Kawaguchi, Takahisa Yamato

  "Stress tensor analysis of the protein quake of photoactive yellow protein"

  2008, Physical Chemistry Chemical Physics

  DOI: 10.1039/B714618C

2007

• Shozo Yokoyama, Takashi Tada, Takahisa Yamato

  "Modulation of the Absorption Maximum of Rhodopsin by Amino Acids in the C-terminus"

  2007, Photochemistry and photobiology

  DOI: 10.1562/2006-06-19-RA-939

• T. Yamato, T. Ishikura, T. Kakitani, K. Kawaguchi, H. Watanabe

  "Spectral tuning of photoactive yellow protein"

  2007, Photochemistry and photobiology

  DOI: 10.1562/2006-06-16-RA-930

2006

• Takakazu Ishikura, Takahisa Yamato

  "Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis"

  2006, Chemical physics letters

  DOI: 10.1016/j.cplett.2006.10.092

• H. Nishioka, T. Yamato, T. Kakitani

  "Temperature dependence of the inelastic electron tunneling"

  2006, Molecular Simulation

  DOI: 10.1080/08927020600835665

• Kazutomo Kawaguchi, Takahisa Yamato

  "Theoretical prediction of optical absorption maxima for photosensory receptor mutants"

  2006, Chemical physics letters

  DOI: 10.1016/j.cplett.2006.08.141

2005

• Hirotaka Nishioka, Akihiro Kimura, Takahisa Yamato, Tsutomu Kawatsu, Toshiaki Kakitani

  "Interference, fluctuation, and alternation of electron tunneling in protein media. 1. Two tunneling routes in photosynthetic reaction center alternate due to thermal fluctuation of protein conformation"

  2005, The Journal of Physical Chemistry B

  DOI: 10.1021/jp046282x

• Hirotaka Nishioka, Akihiro Kimura, Takahisa Yamato, Tsutomu Kawatsu, Toshiaki Kakitani

  "Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-Condon theory for the energy gap dependence of electron transfer rate"

  2005, The Journal of Physical Chemistry B

  DOI: 10.1021/jp051606i

2004

• Atsushi Yamada, Takakazu Ishikura, Takahisa Yamato

  "Direct measure of functional importance visualized atom-by-atom for photoactive yellow protein: Application to photoisomerization reaction"

  2004, Proteins: Structure, Function, and Bioinformatics

  DOI: 10.1002/prot.20063

• Atsushi Yamada, Takakazu Ishikura, Takahisa Yamato

  "Role of protein in the primary step of the photoreaction of yellow protein"

  2004, PROTEINS: Structure, Function, and Bioinformatics

  DOI: 10.1002/prot.20006

• Atsushi Yamada, Takahisa Yamato, Toshiaki Kakitani, Shigeyoshi Yamamoto

  "Torsion Potential Works in Rhodopsin"

  2004, Photochemistry and Photobiology

  DOI: 10.1111/j.1751-1097.2004.tb00037.x

2002

• A Yamada, T Kakitani, S Yamamoto, T Yamato

  "A computational study on the stability of the protonated Schiff base of retinal in rhodopsin"

  2002, Chemical physics letters

  DOI: 10.1016/S0009-2614(02)01649-4

• No Data

  "Analysis of cis-trans photoisomerization mechanism of rhodopsin based on the tertiary structure of rhodopsin"

  2002, Journal of Photoscience

  DOI: nan

• Tsutomu Kawatsu, Toshiaki Kakitani, Takahisa Yamato

  "Destructive interference in the electron tunneling through protein media"

  2002, The Journal of Physical Chemistry B

  DOI: 10.1021/jp026035y

• Tsutomu Kawatsu, Toshiaki Kakitani, Takahisa Yamato

  "On the anomaly of the tunneling matrix element in long-range electron transfer"

  2002, The Journal of Physical Chemistry B

  DOI: 10.1021/jp013975u

• T. Kakitani, T. Kawatsu, A. Kimura, A. Yamada, T. Yamato, S. Yamamoto

  "Unique mechanisms of excitation energy transfer, electron transfer and photoisomerization in biological systems"

  2002, Journal of biological physics

  DOI: 10.1023/A:1020356404203

2001

• A Yamada, S Yamamoto, T Yamato, T Kakitani

  "Ab initio MO study on potential energy surfaces for twisting around C7 C8 and C4--C7 bonds of coumaric acid"

  2001, Journal of Molecular Structure: THEOCHEM

  DOI: 10.1016/S0166-1280(00)00627-8

• Shigeyoshi Yamamoto, Hiroaki Wasada, Toshiaki Kakitani, Takahisa Yamato

  "Ab initio MO study on the potential energy surfaces for twisting around C15N bond of protonated Schiff base of retinal"

  2001, Journal of Molecular Structure: THEOCHEM

  DOI: 10.1016/S0166-1280(00)00842-3

• Tsutomu Kawatsu, Toshiaki Kakitani, Takahisa Yamato

  "Worm model for electron tunneling in proteins: Consolidation of the pathway model and the Dutton plot"

  2001, The Journal of Physical Chemistry B

  DOI: 10.1021/jp003918l

2000

• Akihiro Kimura, Toshiaki Kakitani, Takahisa Yamato

  "Theory of excitation energy transfer in the intermediate coupling case. II. Criterion for intermediate coupling excitation energy transfer mechanism and application to the photosynthetic antenna system"

  2000, The Journal of Physical Chemistry B

  DOI: 10.1021/jp000589o

• Akihiro Kimura, Toshiaki Kakitani, Takahisa Yamato

  "Theory of excitation transfer in the intermediate coupling case"

  2000, Journal of luminescence

  DOI: 10.1016/S0022-2313(99)00424-X

1999

• Shigeyoshi Yamamoto, Hiroaki Wasada, Toshiaki Kakitani, Takahisa Yamato

  "Ab initio MO study on the potential energy surfaces for twisting around the C11 C12 bond of the protonated Schiff base of retinal1"

  1999, Journal of Molecular Structure: THEOCHEM

  DOI: 10.1016/S0166-1280(98)00437-0

• Mitsunori Takano, Takahisa Yamato, Junichi Higo, Akira Suyama, Kuniaki Nagayama

  "Molecular dynamics of a 15-residue poly (L-alanine) in water: helix formation and energetics"

  1999, Journal of the American Chemical Society

  DOI: 10.1021/ja982919c

• Norikazu Goto, Toshiaki Kakitani, Takahisa Yamato, Yasuyo Hatano

  "Monte Carlo simulation study on the structure and reaction at metal-electrolyte interface. II. Mechanism of nonlinear electrode reactions"

  1999, Journal of the Physical Society of Japan

  DOI: 10.1143/jpsj.68.3729

1998

• Takahisa Yamato, Nobuo Niimura, Nobuhiro Go

  "Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore"

  1998, Proteins: Structure, Function, and Bioinformatics

  DOI: 10.1002/(SICI)1097-0134(19980815)32:3%3C268::AID-PROT2%3E3.0.CO;2-E

• H. Wako, T. Yamato

  "Novel method to detect a motif of local structures in different protein conformations."

  1998, Protein engineering

  DOI: 10.1093/protein/11.11.981

1997

• Nobuo Kobayashi, Takahisa Yamato, Nobuhiro Go

  "Mechanical property of a TIM-barrel protein"

  1997, Proteins: Structure, Function, and Bioinformatics

  DOI: 10.1002/(SICI)1097-0134(199705)28:1%3C109::AID-PROT11%3E3.0.CO;2-N

• Takahisa Yamato, Toshiaki Kakitani

  "Molecular Dynamics Simulation of the Excited-State Dynamics of Bacteriorhodopsin"

  1997, Photochemistry and photobiology

  DOI: 10.1111/j.1751-1097.1997.tb03217.x

1996

• Takahisa Yamato

  "Finite element study of protein structure under high pressure"

  1996, Progress in Biotechnology

  DOI: 10.1016/S0921-0423(06)80027-4

• Takahisa Yamato

  "Strain tensor field in proteins"

  1996, Journal of molecular graphics

  DOI: 10.1016/0263-7855(96)00022-7

1994

• No Data

  "Computational Study of Mechanical Constructions of Protein."

  1994, 日本物理学会誌

  DOI: 10.11316/butsuri1946.49.305

• Takahisa Yamato, Minoru Saito, Junichi Higo

  "Topographical metric to analyze the thermal fluctuations of protein conformation"

  1994, Chemical physics letters

  DOI: 10.1016/0009-2614(94)00055-7

1993

• Takahisa Yamato, Jun'ichi Higo, Yasunobu Seno, Nobuhiro Gō

  "Conformational deformation in deoxymyoglobin by hydrostatic pressure"

  1993, Proteins: Structure, Function, and Bioinformatics

  DOI: 10.1002/prot.340160403