Papers - YAMATO, Takahisa

Site-selective heat current analysis of & alpha;-helical protein with linear-homopolymer-like model

Wang Tingting, Yamato Takahisa, Sugiura Wataru

JOURNAL OF CHEMICAL PHYSICS   Vol. 158 ( 21 )   2023.6

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DOI： 10.1063/5.0149362

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Computational study on the thermal conductivity of a protein Reviewed International coauthorship

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

Journal of Physical Chemistry B     2022.4

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： https://doi.org/10.1021/acs.jpcb.2c00958

Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations Invited Reviewed International coauthorship

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

JOURNAL OF PHYSICAL CHEMISTRY B   Vol. 124 ( 44 ) page： 9852 - 9861   2020.11

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jpcb.0c08091

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Variation of Energy Transfer Rates across Protein-Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin Reviewed International coauthorship

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

JOURNAL OF PHYSICAL CHEMISTRY B   Vol. 124 ( 7 ) page： 1148 - 1159   2020.2

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jpcb.9b11413

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Structure, dynamics and energy flow that govern heme protein functions: theory and experiments. Invited Reviewed International coauthorship

T. Yamato, D.M. Leitner

Biophysical Reviews   Vol. 12   page： 291 - 292   2020

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (conference, symposium, etc.)  

DOI： doi.org/10.1007/s12551-020-00625-4

Recent developments in the computational study of protein structural and vibrational energy dynamics Invited Reviewed International coauthorship

D. M. Leitner, T. Yamato

Biophysical Reviews   Vol. 12   page： 317 - 322   2020

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.1007/s12551-020-00661-0

Energy transport network in proteins Invited Reviewed

Takahisa YAMATO

Seibutsu Butsuri   Vol. 60 ( 2 ) page： 94 - 97   2020

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Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.2142/biophys.60.094

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

Ota Kunitaka, Yamato Takahisa

JOURNAL OF PHYSICAL CHEMISTRY B   Vol. 123 ( 4 ) page： 768 - 775   2019.1

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DOI： 10.1021/acs.jpcb.8b10489

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Normal mode analysis and beyond

Yamato Takahisa, Laprevote Olivier

BIOPHYSICS AND PHYSICOBIOLOGY   Vol. 16   page： 322 - 327   2019

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DOI： 10.2142/biophysico.16.0_322

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

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

JOURNAL OF PHYSICAL CHEMISTRY B   Vol. 122 ( 40 ) page： 9331-9339   2018.10

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jpcb.8b07552

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Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited

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

JOURNAL OF PHYSICAL CHEMISTRY B   Vol. 122 ( 27 ) page： 6912-6921   2018.7

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jpcb.8b04333

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

Yamada Tatsuya, Mitaku Shigeki, Yamato Takahisa

CHEMICAL PHYSICS LETTERS   Vol. 691   page： 276-282   2018.1

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.cplett.2017.11.025

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MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS

Leitner David M., Yamato Takahisa

REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 31   Vol. 31   page： 63 - 113   2018

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Language：English   Publishing type：Research paper (scientific journal)  

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Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics Reviewed

T. Yamada, T. Yamato, S. Mitaku

Biophysical Journal   Vol. 111 ( 10 ) page： 2986-2098   2016.11

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.bpj.2016.09.051

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

T. Yamada, T. Yamato, S. Mitaku

Biophysical Journal   Vol. 111   page： 2086-2098   2016.11

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.1016/j.bpj.2016.09.051

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

R. Sato, H. Kitoh-Nishioka, K. Ando, T. Yamato

Chem. Phys. Lett.   Vol. 633   page： 247-251   2015

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Language：English   Publishing type：Research paper (scientific journal)  

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

T. Ishikura, Y. Iwata, T. Hatano, T. Yamato

J. Comput. Chem.   Vol. 36   page： 1709-1718   2015

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

T. Yamato and K. Yura

SEIKAGAKU   Vol. 85 ( 8 ) page： 646-655   2013

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Authorship：Lead author   Language：Japanese  

Atomic stress tensor analysis of proteins Reviewed

T. Ishikura, T. Hatano, T. Yamato

Chemical Physics Letters   Vol. 539-540   page： 144-150   2012.6

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Language：English   Publishing type：Research paper (scientific journal)  

We performed stresstensoranalysis of polypeptides at the atomic level by molecular dynamics simulations. Most of the approaches to stresstensoranalysis of molecules in the literature assume that the interatomic forces are pairwise; however commonly used force-field functions contain multi-body interactions. To address this issue, we derived new mathematical formulae for atomic forces based on force-field functions, in which the total force acting on each atom is expressed as a summation of pairwise interatomic forces. Then, a computer program for stresstensoranalysis was developed, and it successfully characterized the mechanical features of molecules at the atomic level.

DOI： 10.1016/j.cplett.2012.05.005

Ligand migration in myoglobin: A combined study of computer simulation and X-ray crystallography Reviewed

T. Tsuduki, A. Tomita, S. Koshihara, S. Adachi, T. Yamato

Journal of Chemical Physics   Vol. 136 ( 16 ) page： 16501 (9 pages)   2012.4

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1063/1.4704586