CURRICULUM VITAE
NAME:

Sotaro FUCHIGAMI

OFFICE ADDRESS: Physical Biochemistry Laboratory,
Division of Pharmaceutical Sciences,
School of Pharmaceutical Sciences,
University of Shizuoka
52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
Tel: +81-54-264-5642
Fax: +81-54-264-5644
E-mail: sotaro.f@u-shizuoka-ken.ac.jp
EDUCATION:
Apr. 1999 – Nov. 2002:

Apr. 1997 – Mar. 1999:

Apr. 1993 – Mar. 1997:

EXPERIENCE:
Apr. 2023 – present:

Apr. 2018 – Mar. 2023:

Doctor of Philosophy (PhD)
in Department of Multi-Disciplinary Sciences,
Graduate School of Arts and Sciences,
The University of Tokyo, Japan.
Adviser: Associate Professor Kiyohiko Someda
Master of Philosophy (MPhil)in Department of Multi-Disciplinary Sciences,
Graduate School of Arts and Sciences,
The University of Tokyo, Japan.
Adviser: Associate Professor Kiyohiko Someda
Bachelor of Philosophy (BPhil)in Department of Basic Science,
College of Arts and Sciences,
The University of Tokyo, Japan.

Research Assistant Professor
at Division of Pharmaceutical Sciences,
School of Pharmaceutical Sciences,
University of Shizuoka, Japan.
Program-Specific Associate Professor (JST-CREST)
at Division of Biological Sciences,
Graduate School of Science,
Kyoto University, Japan.
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Sotaro Fuchigami

Curriculum vitae

Apr. 2013 – Mar. 2018:Assistant Professor
at Department of Medical Life Science,Graduate School of Medical Life Science,
Yokohama City University, Japan.
Apr. 2009 – Mar. 2013: Assistant Professor
at Department of Supramolecular Biology,
Graduate School of Nanobioscience,
Yokohama City University, Japan.
Apr. 2007 – Mar. 2009: Assistant Professor
at Department of Supramolecular Biology,
International Graduate School of Arts and Sciences,
Yokohama City University, Japan.
Apr. 2005 – Mar. 2007: Research Associate
at Department of Supramolecular Biology,
International Graduate School of Arts and Sciences,
Yokohama City University, Japan.
Apr. 2004 – Mar. 2005: Research Associate
at Science of Biological Supramolecular Systems,
Graduate School of Integrated Science,
Yokohama City University, Japan.
Dec. 2002 – Mar. 2004: Post-doctoral Fellowof ACT-JST (Research and Development for Applying
Advanced Computational Science and Technology,
Japan Science and Technology Corporation)
at Department of Chemistry, Faculty of Science,
Kobe University, Japan.

PUBLICATIONS:
1. Tsuyoshi Ishizone*, Yasuhiro Matsunaga, Sotaro Fuchigami, and Kazuyuki
Nakamura, “Representation of protein dynamics disentangled by timestructure-based prior.” J. Chem. Theory Comput. 20(1) 436–450, 2024.
2. Kazumi Saikusa*, Daiki Asakawa, Sotaro Fuchigami, and Satoko Akashi,“Evaluation for ion heating of H2A-H2B dimer in ion mobility spectrometry–mass spectrometry.” Mass Spectrom. (Tokyo) 12(1) A0131-1-8, 2023.
3. Suguru Kato, Shoji Takada,* and Sotaro Fuchigami*, “Particle smoother toassimilate asynchronous movie data of high-speed AFM with MD
simulations.” J. Chem. Theory Comput. 19(14) 4678–4688, 2023.
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Curriculum vitae

4. Yasuhiro Matsunaga*, Sotaro Fuchigami, Tomonori Ogane, Shoji Takada,“End-to-end differentiable blind tip reconstruction for noisy atomic force
microscopy images.” Sci. Rep. 13(1) 129-1-16, 2023.
5. Sotaro Fuchigami*, Shoji Takada*, “Inferring Conformational State of Myosin
Motor in an Atomic Force Microscopy Image via Flexible Fitting MolecularSimulations.” Front. Mol. Biosci. 9, 882989-1-8, 2022.
6. Sotaro Fuchigami*, Toru Niina, Shoji Takada*, “Case Report: Bayesian
Statistical Inference of Experimental Parameters via Biomolecular
Simulations: Atomic Force Microscopy.” Front. Mol. Biosci. 8, 636940-1-6,2021.
7. Sotaro Fuchigami*, Toru Niina, Shoji Takada*, “Particle filter method tointegrate high-speed atomic force microscopy measurements withbiomolecular simulations.” J. Chem. Theory Comput. 16(10) 6609–6619,2020.
8. Toru Niina, Sotaro Fuchigami, Shoji Takada*, “Flexible fitting of biomolecularstructures to atomic force microscopy images via biased molecularsimulations.” J. Chem. Theory Comput. 16(2) 1349-1358, 2020.
9. Ikuko Hayashi*, Takashi Oda, Mamoru Sato, Sotaro Fuchigami,“Cooperative DNA binding of the plasmid partitioning protein TubR from theBacillus cereus pXO1 plasmid.” J. Mol. Biol. 430(24) 5015-5028, 2018.
10. Kazumi Saikusa, Akihisa Osakabe, Daiki Kato, Sotaro Fuchigami, AritakaNagadoi, Yoshifumi Nishimura, Hitoshi Kurumizaka, Satoko Akashi*,“Structural diversity of nucleosomes characterized by native massspectrometry.” Anal. Chem. 90(13) 8217-8226, 2018.
11. Takahisa Maki, Ashley D. Grimaldi, Sotaro Fuchigami, Irina Kaverina, Ikuko
Hayashi*, “CLASP2 has two distinct TOG domains that contribute differently
to microtubule dynamics.” J. Mol. Biol. 427(14) 2379-2395, 2015.
12. Kazumi Saikusa, Aritaka Nagadoi, Kana Hara, Sotaro Fuchigami, Hitoshi
Kurumizaka, Yoshifumi Nishimura, and Satoko Akashi*, “Mass spectrometricapproach for characterizing the disordered tail regions of the histone
H2A/H2B dimer.” Anal. Chem. 87(4) 2220-2227, 2015.
13. Yusuke Naritomi, Sotaro Fuchigami*, “Slow dynamics of a protein backbone
in molecular dynamics simulation revealed by time-structure based
independent component analysis.” J. Chem. Phys. 139(21) 215102-1-10,
2013.
14. Kazumi Saikusa, Sotaro Fuchigami, Kyohei Takahashi, Yuuki Asano, Aritaka
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Curriculum vitae

Nagadoi, Hiroaki Tachiwana, Hitoshi Kurumizaka, Mitsunori Ikeguchi,
Yoshifumi Nishimura*, and Satoko Akashi*, “Gas-phase structure of thehistone multimers characterized by ion mobility mass spectrometry andmolecular dynamics simulation.” Anal. Chem. 85(8) 4165-4171, 2013.
15. Sotaro Fuchigami, Hiroshi Fujisaki, Yasuhiro Matsunaga and Akinori
Kidera*, “Protein functional motions: basic concepts and computationalmethodologies.” Adv. Chem. Phys. 145 35-82, 2011.
16. Takayuki Amemiya, Ryotaro Koike, Sotaro Fuchigami, Mitsunori Ikeguchi
and Akinori Kidera*, “Classification and annotation of the relationshipbetween protein structural change and ligand binding.” J. Mol. Biol. 408(3)568-584, 2011.
17. Yusuke Naritomi, Sotaro Fuchigami*, “Slow dynamics in protein fluctuations
revealed by time-structure based independent component analysis: Thecase of domain motions.” J. Chem. Phys. 134(6) 065101-1-8, 2011.
18. Koro Nishikata, Sotaro Fuchigami, Mitsunori Ikeguchi and Akinori Kidera*,“ Molecular modeling of the HAMP domain of sensory rhodopsin II
transducer from Natronomonas pharaonis.” BIOPHYSICS 6 27-36, 2010.
19. Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, and Akinori Kidera*,“Latent dynamics of a protein molecule observed in dihedral angle space.”
J. Chem. Phys. 132(11) 115103-1-7, 2010.
20. Sotaro Fuchigami*, Satoshi Omori, Mitsunori Ikeguchi, and Akinori Kidera*,“Normal mode analysis of protein dynamics in a non-Eckart frame.” J.
Chem. Phys. 132(10) 104109-1-7, 2010.
21. Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, and Akinori Kidera*,“Linear response theory in dihedral angle space for protein structuralchange upon ligand binding.” J. Comput. Chem. 30(16) 2602-2608, 2009.
22. Yasuhiro Matsunaga, Sotaro Fuchigami, and Akinori Kidera*, “Multivariate
frequency domain analysis of protein dynamics.” J. Chem. Phys. 130(12)124104-1-8, 2009.
23. Christine Addy, Masato Ohara, Fumihiro Kawai, Akinori Kidera, MitsunoriIkeguchi, Sotaro Fuchigami, Masanori Osawa, Ichio Shimada, Sam-YongPark, Jeremy R. H. Tame and Jonathan G. Heddle*, “Nickel binding to NikA:
an additional binding site reconciles spectroscopy, calorimetry andcrystallography.” Acta Cryst. D63(2) 221-229, 2007.
24. Sotaro Fuchigami*, Kiyohiko Someda*, “Nonadiabatic dynamics of theclassical hydrogen molecular ion H2+.” J. Phys. Soc. Jpn. 72(8) 1891-1898,
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Curriculum vitae

2003.
25. Kiyohiko Someda*, Sotaro Fuchigami, “Secular dynamics in intramolecularvibrational energy redistribution and secular increase of relative entropy.” J.
Phys. Chem. A 102(47) 9454-9463, 1998.

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