| 1. |
Koichiro Kato, Ami Yamamoto, Chiduru Watanabe, Kaori Fukuzawa, Application of Model Core Potentials to Zn- and Mg-containing Metalloproteins in the Fragment Molecular Orbital Method, Chem-Bio Informatics Journal, https://doi.org/10.1273/cbij.23.14, 23, 14-25, 2023.09. |
| 2. |
Boda Yu, Sadahito Naka, Haruka Aoki, Koichiro Kato, Daiki Yamashita, Shun Fujii, Yuichiro K. Kato, Tsuyohiko Fujigaya, Tomohiro Shiraki, ortho-Substituted Aryldiazonium Design for the Defect Configuration-Controlled Photoluminescent Functionalization of Chiral Single-Walled Carbon Nanotubes, ACS Nano, 10.1021/acsnano.2c09897, 2022.12. |
| 3. |
Takashi Miyano, Ryosuke Kaneko, Toshihide Kimura, Misa Maruoka, Akihiro Kishimura, Koichiro Kato, Michiko Furuta, Yoshihisa Yamashita, Dietary Problems Are Associated with Frailty Status in Older People with Fewer Teeth in Japan, International Journal of Environmental Research and Public Health, 10.3390/ijerph192316260, 2022.12. |
| 4. |
Kaori Fukuzawa, Koichiro Kato, Chiduru Watanabe, Yusuke Kawashima, Yuma Handa, Ami Yamamoto, Kazuki Watanabe, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Teruki Honma, Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins, Journal of Chemical Information and Modeling, 10.1021/acs.jcim.1c00694, 2021.09. |
| 5. |
Yuji Mochizuki, Tatsuya Nakano, Kota Sakakura, Yoshio Okiyama, Hiromasa Watanabe, Koichiro Kato, Yoshinobu Akinaga, Shinya Sato, Jun-inchi Yamamoto, Katsumi Yamashita, Tadashi Murase, Takeshi Ishikawa, Yuto Komeiji, Yuji Kato, Naoki Watanabe, Takashi Tsukamoto, Hirotoshi Mori, Koji Okuwaki, Shigenori Tanaka, Akifumi Kato, Chiduru Watanabe, Kaori Fukuzawa, The ABINIT-MP Program, Recent Advances of the Fragment Molecular Orbital Method, 10.1007/978-981-15-9235-5_4, 53-67, 2021.01. |
| 6. |
Koichiro Kato, Aya Hashimoto, Eiichi Tamiya, Kaori Fukuzawa, Yuichiro Ishikawa, Yuji Mochizuki, Modeling of Solid and Surface, Recent Advances of the Fragment Molecular Orbital Method, 10.1007/978-981-15-9235-5_21, 407-424, 2021.01. |
| 7. |
Koichiro Kato, Teruki Honma, Kaori Fukuzawa, Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation, Journal of Molecular Graphics and Modelling, 10.1016/j.jmgm.2020.107695, 100, 107695-107695, 2020.11, 世界的に猛威を振るうCOVID-19について、治療薬やワクチンの研究開発が進められている。そんな中2020年4月22日に、有望な治療薬であるレムデシビルとSARS-CoV-2のRNA依存RNAポリメラーゼ（RdRp）が結合した構造が公開された。本論文は先述のRdRp－レムデシビル複合体構造の量子化学的な解析を即座に実施し、レムデシビルが安定的にRdRpに結合する理由を明らかにした。. |
| 8. |
Koichiro Kato, Tomohide Masuda, Chiduru Watanabe, Naoki Miyagawa, Hideo Mizouchi, Shumpei Nagase, Kikuko Kamisaka, Kanji Oshima, Satoshi Ono, Hiroshi Ueda, Atsushi Tokuhisa, Ryo Kanada, Masateru Ohta, Mitsunori Ikeguchi, Yasushi Okuno, Kaori Fukuzawa, Teruki Honma, High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning, Journal of Chemical Information and Modeling, 10.1021/acs.jcim.0c00273, 60, 7, 3361-3368, 2020.07. |
| 9. |
Yoshinobu Akinaga, Koichiro Kato, Tatsuya Nakano, Kaori Fukuzawa, Yuji Mochizuki, Fragmentation at sp 2 carbon atoms in fragment molecular orbital method, Journal of Computational Chemistry, 10.1002/jcc.26190, 41, 15, 1416-1420, 2020.06. |
| 10. |
Ryo HATADA, Kouichiro KATO, Koji OKUWAKI, Kaori FUKUZAWA, Yuji MOCHIZUKI, Interaction Analyses between Calcite/Apatite and Peptides by Fragment Molecular Orbital Method, Journal of Computer Chemistry, Japan, 10.2477/jccj.2019-0030, 19, 1, 1-7, 2020.06. |
| 11. |
Kotaro Koiwai, Kazue Inaba, Kana Morohashi, Sora Enya, Reina Arai, Hirotatsu Kojima, Takayoshi Okabe, Yuuta Fujikawa, Hideshi Inoue, Ryunosuke Yoshino, Takatsugu Hirokawa, Koichiro Kato, Kaori Fukuzawa, Yuko Shimada-Niwa, Akira Nakamura, Fumiaki Yumoto, Toshiya Senda, Ryusuke Niwa, An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo., The Journal of biological chemistry, 10.1074/jbc.RA119.011463, 295, 20, 7154-7167, 2020.05, Ecdysteroids are the principal steroid hormones essential for insect development and physiology. In the last 18 years, several enzymes responsible for ecdysteroid biosynthesis encoded by Halloween genes were identified and genetically and biochemically characterized. However, the tertiary structures of these proteins have not yet been characterized. Here, we report the results of an integrated series of in silico, in vitro, and in vivo analyses of the Halloween GST protein Noppera-bo (Nobo). We determined crystal structures of Drosophila melanogaster Nobo (DmNobo) complexed with GSH and 17β-estradiol, a DmNobo inhibitor. 17β-Estradiol almost fully occupied the putative ligand-binding pocket and a prominent hydrogen bond formed between 17β-estradiol and Asp-113 of DmNobo. We found that Asp-113 is essential for 17β-estradiol-mediated inhibition of DmNobo enzymatic activity, as 17β-estradiol did not inhibit and physically interacted less with the D113A DmNobo variant. Asp-113 is highly conserved among Nobo proteins, but not among other GSTs, implying that this residue is important for endogenous Nobo function. Indeed, a homozygous nobo allele with the D113A substitution exhibited embryonic lethality and an undifferentiated cuticle structure, a phenocopy of complete loss-of-function nobo homozygotes. These results suggest that the nobo family of GST proteins has acquired a unique amino acid residue that appears to be essential for binding an endogenous sterol substrate to regulate ecdysteroid biosynthesis. To the best of our knowledge, ours is the first study describing the structural characteristics of insect steroidogenic Halloween proteins. Our findings provide insights relevant for applied entomology to develop insecticides that specifically inhibit ecdysteroid biosynthesis.. |
| 12. |
Koichiro Kato, Yuki Maekawa, Naoki Watanabe, Kenji Sasaoka, Takahiro Yamamoto, Discovery of new microscopic structures in surface water on graphene using data science, Japanese Journal of Applied Physics, 10.7567/1347-4065/ab6564, 59, 2, 025001-025001, 2020.02. |
| 13. |
Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki, Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method, Japanese Journal of Applied Physics, 10.7567/1347-4065/ab5335, 58, 12, 120906-120906, 2019.12. |
| 14. |
Yuji MOCHIZUKI, Yoshinobu AKINAGA, Kota SAKAKURA, Hiromasa WATANABE, Kouichiro KATO, Naoki WATANABE, Koji OKUWAKI, Tatsuya NAKANO, Kaori FUKUZAWA, Current Status of ABINIT-MP Open Series, Journal of Computer Chemistry, Japan, 10.2477/jccj.2019-0016, 18, 3, 129-131, 2019.10. |
| 15. |
Masahiko Machida, Koichiro Kato, Motoyuki Shiga, Nuclear quantum effects of light and heavy water studied by all-electron first principles path integral simulations, The Journal of Chemical Physics, 10.1063/1.5000091, 148, 10, 102324-102324, 2018.03. |
| 16. |
Yuji MOCHIZUKI, Kota SAKAKURA, Yoshinobu AKINAGA, Kouichiro KATO, Hiromasa WATANABE, Yoshio OKIYAMA, Tatsuya NAKANO, Yuto KOMEIJI, Akira OKUSAWA, Kaori FUKUZAWA, Shigenori TANAKA, Current Status of ABINIT-MP as a FMO Program and Related Works with Machine Learning, Journal of Computer Chemistry, Japan, 10.2477/jccj.2017-0051, 16, 5, 119-122, 2018.01. |
| 17. |
Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki, Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method, Chemical Physics Letters, 10.1016/j.cplett.2015.03.057, 629, 58-64, 2015.06, Abstract We have applied the four-body corrected fragment molecular orbital (FMO4) calculations to analyze the interaction between a designed peptide motif (Glu1-Ser2-Gln3-Glu4-Ser5) and the hydroxyapatite (HA) solid mimicked by a cluster model consisting of 1408 atoms. To incorporate statistical fluctuations, a total of 30 configurations were generated through classical molecular dynamics simulation with water molecules and were subjected to FMO4 calculations at the MP2 level. It was found that Ser5 plays a leading role in interacting with the phosphate moieties of HA via charge transfer and also that negatively charged Glu1 and Glu4 provide electrostatic stabilizations with the calcium ions.. |
| 18. |
Koichiro Kato, Takashi Koretsune, Susumu Saito, Energetics and electronic properties of twisted single-walled carbon nanotubes, Physical Review B - Condensed Matter and Materials Physics, 10.1103/PhysRevB.85.115448, 85, 11, 2012.03, We perform a systematic first-principles study of energetics and electronic properties of chiral carbon nanotubes (CNTs) in the density-functional theory. It is found that chiral CNTs possess slightly twisted ground-state geometries. Moderate-diameter CNTs show twisting-dependent electronic properties well classified by their chiral indices, while the electronic structures of small-diameter CNTs possess sizable but individually different twisting dependences, leading to metal-semiconductor transitions in some CNTs. The CNT having the widest fundamental gap is predicted to be the twisted (4,3) CNT. © 2012 American Physical Society.. |
| 19. |
Koichiro Kato, Takashi Koretsune, Susumu Saito, Twisting Effects on Carbon Nanotubes: A First-Principles Study with Helical Symmetry Operations, Journal of Physics: Conference Series, 10.1088/1742-6596/302/1/012007, 302, 012007-012007, 2011.07. |
| 20. |
Koichiro Kato, Susumu Saito, Geometries, electronic structures and energetics of small-diameter single-walled carbon nanotubes, Physica E: Low-Dimensional Systems and Nanostructures, 10.1016/j.physe.2010.07.025, 43, 3, 669-672, 2011.01, We study the detailed geometries, electronic structures and energetics of small-diameter single-walled carbon nanotubes in the framework of the density functional theory with the local density approximation. In the present work, we study 41 kinds of nanotubes including 16 chiral nanotubes. It is found that electronic properties of optimized nanotubes as well as their geometrical properties depend strongly on not only diameter but also chiral angle. The largest difference from graphene values for both bond lengths and bond angles is found in zigzag nanotubes among all the nanotubes with similar diameters. Interestingly, the bond length decreases relative to that of graphene when the angle between the bond direction and tube axis is less than about 22°. As for the electronic structures, because of significant curvature effect, the band gap values of small-diameter nanotubes are show significant deviation from the classification from the tight-binding study. Interestingly, we also find that so-called "near-armchair" nanotubes have large band gaps even in the small-diameter region. © 2010 ElsevierB.V. All rights reserved.. |
| 21. |
Koichiro Kato, Susumu Saito, Systematic Study of Work Functions of Single-walled Carbon Nanotubes, MRS Proceedings, 10.1557/proc-1204-k18-02, 1204, 2009.12, AbstractThe work function is one of the crucial quantities in understanding their field emission properties and applying carbon nanotubes to electronic devices. We perform the systematic study of work functions of 44 kinds of isolated single-walled carbon nanotubes in the framework of the density functional theory. It has been revealed that the first-principles study plays a very important role for predicting various properties of carbon nanotubes. In general, we have to perform the structural relaxation in order to know the accurate electronic properties of carbon nanotubes. Therefore we carry out the complete geometrical relaxations for 44 kinds of carbon nanotubes and evaluate their work functions. The diameters (D) of nanotubes studied satisfy 0.3 |
| 22. |
Yasuhiko Tanaka, Yasuhiko Hirana, Yasuro Niidome, Koichiro Kato, Susumu Saito, Naotoshi Nakashima, Experimentally determined redox potentials of individual (n,m) single-walled carbon nanotubes, Angewandte Chemie - International Edition, 10.1002/anie.200902468, 48, 41, 7655-7659, 2009.09, Nanotubes reveal their potential: The fabrication of a thin film that retains isolated singlewalled nanotubes (SWNTs) allows the experimental determination of the redox potentials of many individual SWNTs that have different chirality indexes (n,m). The method is simple and applicable to all individual SWNTs whose near-IR photoluminescence (PL) is detectable (see picture). © 2009 Wiley-VCH Verlag GmbH &
Co. KGaA.. |
