KURITA Noriyuki

J-GLOBAL         Last updated: Aug 21, 2019 at 17:35
 
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Name
KURITA Noriyuki
Affiliation
Toyohashi University of Technology
Section
Faculty of Engineering, Department of Knowledge-Based Information Engineering
Job title
Associate Professor
Degree
Doctor(Engineering)(University of Tsukuba)

Research Areas

 

Academic & Professional Experience

 
Apr 2007
 - 
Today
Associate professor, Department of Compue\ter Science and Engineering, Toyohashi University of Technology
 
1996
 - 
2002
Lecturer, Toyohashi Univ. of Technology
 
2002
   
 
- Associate Prof., Toyohashi Univ. of Technology
 
1989
 - 
1996
Researcher, Hitachi, Energy Research
 
 
   
 
Laboratory,
 

Education

 
 
 - 
Mar 1989
Materials science, Department of engineering, Tsukuba University
 
 
 - 
1989
Materials Science, Graduate School, Division of Engineering, University of Tsukuba
 
 
 - 
Mar 1984
Applied physics, Department of science, Science university of Tokyo
 
 
 - 
1984
Applied Physics, Faculty of Science, Tokyo University of Science
 

Published Papers

 
Change in binding states between catabolite activating protein and DNA induced by ligand-binding: molecular dynamics and ab initio fragment molecular orbital calculations
Anan, R.; Nakamura, T.; Shimamura, K.; Matsushita, Y.; Ohyama, T.; Kurita, N.
Journal of Molecular Modeling      2019   [Refereed]
Specific interactions between 2-trans enoyl-acyl carrier protein reductase and its ligand: protein-ligand docking and ab initio fragment molecular orbital calculations
Phusi, N.; Sato, R.; Ezawa, T.; Tomioka, S.; Hanwarinroj, C.; Khamsri, B.; Kamsri, P.; Punkvang, A.; Pungpo, P.; Kurita, N.
Journal of Molecular Graphics and Modelling   88 299-308   2019   [Refereed]
Effect of Zn ion on the structure and electronic states of Aβ nonamer: molecular dynamics and ab initio molecular orbital calculations
Tomioka, S.; Sogawa, H.; Shinzato, T.; Ishimura, H.; Okamoto, A.; Blume, Y.; Shulga, S.; Kurita, N.
Molecular Simulation   45 706-715   2019   [Refereed]
Ryosuke Takeda, Rie Suzuki, Ittetsu Kobayashi, Kentaro Kawai, Atsushi Kittaka, Midori Takimoto-Kamimura, Noriyuki Kurita
Chem-Bio Informatics Journal   18 32-43   Mar 2018   [Refereed]
© 2018, Chem-Bio Informatics Society. All rights reserved. The chirality of a compound affects its biochemical and pharmaceutical properties. It was found that the binding affinity between vitamin D receptor (VDR) and its ligand depends significan...
Ryosuke Takeda, Ittetsu Kobayashi, Rie Suzuki, Kentaro Kawai, Atsushi Kittaka, Midori Takimoto-Kamimura, Noriyuki Kurita
Journal of Molecular Graphics and Modelling   80 320-326   Mar 2018   [Refereed]
© 2018 Elsevier Inc. Vitamin D plays an important role in the regulation of the calcium and phosphorus metabolism as well as in bone formation. These physiological actions caused by vitamin D are triggered by the specific binding of vitamin D to i...
Mitsuki Fujimori, Haruki Sogawa, Shintaro Ota, Pavel Karpov, Sergey Shulga, Yaroslav Blume, Noriyuki Kurita
Chemical Physics Letters   692 166-173   Jan 2018   [Refereed]
© 2017 Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigate...
Shintaro Ota, Shougo Tomioka, Haruki Sogawa, Riku Satou, Mitsuki Fujimori, Pavel Karpov, Sergey Shulga, Yaroslav Blume, Noriyuki Kurita
Chem-Bio Informatics Journal   18 44-57   Jan 2018   [Refereed]
© 2018, Chem-Bio Informatics Society. All rights reserved. Curcumin can bind to tubulin and inhibit the formation of tubulin polymer, which contributes to the formation of microtubule. Binding sites of curcumin on the α- and β-tubulin heterodimer ...
Ligand chirality can affect histidine protonation of vitamin-D receptor: ab initio molecular orbital calculations in water
Terauchi, Y.; Suzuki, R.; Takeda, R.; Kobayashi, I.; Kittaka, A.; Takimoto-Kamimura, M.; Kurita, N.
Journal of Steroid Biochemistry and Molecular Biology   186 89-95   2019   [Refereed]
Shogo Tomioka, Haruki Sougawa, Hiromi Ishimura, Akisumi Okamoto, Noriyuki Kurita, Sergiy Shulga, Pavel Karpov, Yaroslav Blume
Proceedings - 2017 International Conference on Advanced Informatics: Concepts, Theory and Applications, ICAICTA 2017      Oct 2017   [Refereed]
© 2017 IEEE. The accumulation of amyloid beta (Aβ) oligomers and fibrils in a brain is deeply involved as a major cause of the onset of Alzheimer's disease (AD). Recently, solid state NMR analysis for the tissues obtained from AD patient's brain h...
Shintaro Ota, Mitsuki Fujimori, Hiromi Ishimura, Sergiy Shulga, Noriyuki Kurita
Chemical Physics Letters   685 482-489   Oct 2017   [Refereed]
© 2017 Elsevier B.V. Accumulation of amyloid-β (Aβ) peptides in a brain is closely related with the pathogenesis of Alzheimer's disease. To suppress the production of Aβ peptides, we propose novel curcumin derivatives and investigate their binding...
Ittetsu Kobayashi, Ryosuke Takeda, Rie Suzuki, Kanako Shimamura, Hiromi Ishimura, Ryushi Kadoya, Noriyuki Kurita, Kentaro Kawai, Midori Takimoto-Kamimura
Journal of Molecular Graphics and Modelling   75 383-389   Aug 2017   [Refereed]
© 2017 Elsevier Inc. The Androgen Receptor (AR) is a family of nuclear receptor proteins and a ligand-activated transcription factor. Since its abnormal activation can cause the progression of prostate cancer, numerous types of antagonists against...
Ayami Ara, Ryushi Kadoya, Hiromi Ishimura, Kanako Shimamura, Ingebrigt Sylte, Noriyuki Kurita
Journal of Molecular Graphics and Modelling   75 277-286   Aug 2017   [Refereed]
© 2017 Elsevier Inc. Bacteria secrete the enzyme pseudolysin (PLN) to degrade exocellular proteins, and the produced peptides are used as a nutrient for the bacteria. It is thus expected that inhibition of PLN can suppress bacterial growth. Since ...
Ryosuke Takeda, Ittetsu Kobayashi, Kanako Shimamura, Hiromi Ishimura, Ryushi Kadoya, Kentaro Kawai, Atsushi Kittaka, Midori Takimoto-Kamimura, Noriyuki Kurita
Journal of Steroid Biochemistry and Molecular Biology   171 75-79   Jul 2017   [Refereed]
© 2017 Elsevier Ltd Vitamin D is recognized to play important roles not only in the bone metabolism and the regulation of Ca amount in the blood but also in the onset of immunological diseases. These physiological actions caused by vitamin D are t...
Hiromi Ishimura, Shogo Tomioka, Ryushi Kadoya, Kanako Shimamura, Akisumi Okamoto, Sergiy Shulga, Noriyuki Kurita
Chemical Physics Letters   672 13-20   Jan 2017   [Refereed]
© 2017 Elsevier B.V. The accumulation of amyloid-beta (Aβ) aggregates in brain contributes to the onset of Alzheimer's disease (AD). Recent structural analysis for the tissue obtained from AD patients revealed that Aβ aggregates have a single stru...
Yuki Yamada, Seiji Kanayama, Fuminori Ito, Noriyuki Kurita, Hiroshi Kobayashi
Biomedical Reports   7 221-225   Jan 2017   [Refereed]
© 2017, Spandidos Publications. All rights reserved. The receptor for the urokinase-type plasminogen activator (uPA), uPAR, facilitates tumor cell invasion and metastasis by focusing on several ligands, including uPA, integrins and vitronectin. Wi...
Mitsuki Fujimori, Ryushi Kadoya, Shintaro Ota, Noriyuki Kurita, Karpov Pavel, Yaroslav Blume
4th IGNITE Conference and 2016 International Conference on Advanced Informatics: Concepts, Theory and Application, ICAICTA 2016      Dec 2016   [Refereed]
© 2016 IEEE. Filamenting temperature-sensitive mutant Z (FtsZ) is recognized to be essential for performing bacteria cell division. Since the inhibition of activity and polymerization of FtsZ prevents the mycobacteria reproduction, five types of F...
Ittetsu Kobayashi, Kanako Shimamura, Hiromi Ishimura, Ryushi Kadoya, Noriyuki Kurita, Kentaro Kawai, Midori Takimoto-Kamimura
4th IGNITE Conference and 2016 International Conference on Advanced Informatics: Concepts, Theory and Application, ICAICTA 2016      Dec 2016   [Refereed]
© 2016 IEEE. To elucidate the effect of cofactor YLO on the structure and electronic properties of the androgen receptor (AR) and its ligand (TES) complex, we investigate the change in structure for the AR+TES and the AR+TES+YLO complexes by molec...
Hiromi Ishimura, Ryushi Kadoya, Kanako Shimamura, Shintarou Ota, Mitsuki Fujimori, Akisumi Okamoto, Noriyuki Kurita, Sergiy Shulga
4th IGNITE Conference and 2016 International Conference on Advanced Informatics: Concepts, Theory and Application, ICAICTA 2016      Dec 2016   [Refereed]
© 2016 IEEE. The accumulation of amyloid-beta (Aβ) fibrils in a brain has been recognized to contribute to the onset of Alzheimer's disease (AD). However, the relation between the structure of the aggregate and its toxicity to AD patients remains ...
Kanako Shimamura, Hiromi Ishimura, Ittetsu Kobayashi, Ryushi Kadoya, Noriyuki Kurita, Kentaro Kawai, Midori Takimoto-Kamimura
4th IGNITE Conference and 2016 International Conference on Advanced Informatics: Concepts, Theory and Application, ICAICTA 2016      Dec 2016   [Refereed]
© 2016 IEEE. To reveal the effect of water molecules on the specific interactions between androgen receptor (AR) and ligand as well as cofactor, we investigated dynamical properties of the complex by the classical molecular dynamics simulations in...
Ryushi Kadoya, Mitsuki Fujimori, Ryosuke Takeda, Tatsuro Mizushima, Noriyuki Kurita, Pharit Kamsri, Pijittra Meewong, Pornpan Pungpo
4th IGNITE Conference and 2016 International Conference on Advanced Informatics: Concepts, Theory and Application, ICAICTA 2016      Dec 2016   [Refereed]
© 2016 IEEE. Tuberculosis remains a major global health problem caused by Mycobacterium tuberculosis. Cytochrome P450 enzymes such as CYP130 have an intimate involvement in pathogenesis of tuberculosis. It was demonstrated that azole compounds suc...
Ryosuke Takeda, Ryushi Kadoya, Ittetsu Kobayashi, Noriyuki Kurita, Pharit Kamsri, Pijittra Meewong, Pornpan Pungpo
4th IGNITE Conference and 2016 International Conference on Advanced Informatics: Concepts, Theory and Application, ICAICTA 2016      Dec 2016   [Refereed]
© 2016 IEEE. The reverse transcriptase (RT) existing in HIV has been recognized to play an essential role for increasing HIV. It is thus expected that inhibition of the RT activity prevents the increase of HIV. Many types of diarylpyrimidines were...
Shintaro Ota, Hiromi Ishimura, Mitsuki Fujimori, Noriyuki Kurita, Sergiy Shulga
4th IGNITE Conference and 2016 International Conference on Advanced Informatics: Concepts, Theory and Application, ICAICTA 2016      Dec 2016   [Refereed]
© 2016 IEEE. Accumulation of amyloid-β (Aβ) peptides in a brain is closely related with the pathogenesis of Alzheimer's disease. To suppress the production of Aβ peptides, many kinds of agents have been developed for inhibiting the cleavage of amy...
Kanako Shimamura, Naoko Okutsu, Eisuke Shimizu, Sergiy Shulga, Yaroslav B. Blume, Victor I. Danilov, Noriyuki Kurita
Structural Chemistry   27 1793-1806   Dec 2016   [Refereed]
© 2016, Springer Science+Business Media New York. To elucidate the influence of solvating water molecules on the attacking mechanism of OH-radical to DNA base pairs (G–C and A–T), we investigated the reaction mechanism in water, by the use of the ...
N. Okutsu, K. Shimamura, E. Shimizu, S. Shulga, V. I. Danilov, N. Kurita
AIP Conference Proceedings   1709    Feb 2016
© 2016 AIP Publishing LLC. To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approxima...
Hideaki Tamai, Naoko Okutsu, Yuki Tokuyama, Eisuke Shimizu, Satoshi Miyagi, Sergiy Shulga, Victor I. Danilov, Noriyuki Kurita
Molecular Simulation   42 122-130   Jan 2016   [Refereed]
© 2016 © 2015 Taylor & Francis. The dependence of geometric structure and thermal stability of liposomes on their component phospholipid molecules and distribution of molecules in the inner and the outer layers of the liposome is investigated by...
Yuki Matsushita, Takeru Murakawa, Kanako Shimamura, Tatsuya Ohyama, Masato Oishi, Noriyuki Kurita
Molecular Simulation   42 242-256   Jan 2016   [Refereed]
© 2015 Taylor & Francis. Lactose repressor protein (LacR) plays an essential role in controlling the transcription mechanism of genomic information from DNA to mRNA. It has been elucidated that a ligand binding to LacR regulates allosterically t...
Satoshi Miyagi, Kyoshiro Murata, Kazuya Sashino, Satoshi Sawamura, Saeko Uruno, Seiko Yoshimura, Eiichi Akahoshi, Mitsuko Ishihara-Sugano, Satoshi Itoh, Noriyuki Kurita
Molecular Simulation   41 555-563   Jan 2015   [Refereed]
© 2014 Taylor & Francis. Aryl hydrocarbon receptor (AhR) plays critical roles in cell differentiation, and its mechanism is controlled by exogenous and endogenous ligands. However, structures of AhR and its complex with ligand have not been dete...
Hiromi Ishimura, Ryushi Kadoya, Tomoya Suzuki, Takeru Murakawa, Sergiy Shulga, Noriyuki Kurita
Chemical Physics Letters   633 139-145   Jan 2015   [Refereed]
© 2015 Elsevier B.V. All rights reserved. tAlzheimer's disease is caused by accumulation of amyloid- β (Aβ) peptides in a brain. To suppress theproduction of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) b...
Shimizu E, Tokuyama Y, Okutsu N, Nomura K, Danilov VI, Kurita N
Journal of biomolecular structure & dynamics   33(1) 158-166   2015   [Refereed]
Murakawa T, Matsushita Y, Suzuki T, Khan MT, Kurita N
Journal of molecular graphics & modelling   54 54-61   Nov 2014   [Refereed]
Takuya Sugimoto, Tatsuroh Mizushima, Akisumi Okamoto, Noriyuki Kurita
Chemical Physics Letters   612 295-301   Sep 2014   [Refereed]
We investigated structures and electronic properties of model systems for metal organic frameworks (MOFs), using density functional theory (DFT) and fragment molecular orbital (FMO) calculations. The DFT calculations reveal that the MOFs composed ...
Mizushima T, Sugimoto T, Kasumi T, Araki K, Kobayashi H, Kurita N
Journal of molecular modeling   20(6) 2292   Jun 2014   [Refereed]
Okamoto A, Yano A, Nomura K, Higai S, Kurita N
Journal of molecular graphics & modelling   50 113-124   May 2014   [Refereed]
Atsushi Yano, Akisumi Okamoto, Kazuya Nomura, Shin'Ichi Higai, Noriyuki Kurita
Chemical Physics Letters   595-596 242-249   Mar 2014   [Refereed]
We searched stable conformations of amyloid-β (Aβ) dimers composed of Aβ(1-42) or Aβ(1-43) protein in water by replica-exchange molecular dynamics simulations and found that Thr43 of the C-terminal of Aβ(1-43) is hydrogen bonded to Arg5 of the sam...
Tomoyo Kasumi, Kohta Araki, Tatsuya Ohyama, Shingo Tsuji, Eri Yoshikawa, Hiroshi Kobayashi, Noriyuki Kurita
Molecular Simulation   39 769-779   Sep 2013   [Refereed]
Binding of urokinase-type plasminogen activator (uPA) to its receptor (uPAR) on the surface of a cancer cell is considered to be a trigger for starting cancer invasions. In addition, the somatomedin B (SMB) domain of vitronectin binds simultaneous...
Akisumi Okamoto, Atsushi Yano, Kazuya Nomura, Shin'Ichi Higai, Noriyuki Kurita
Chemical Physics Letters   577 131-137   Jul 2013   [Refereed]
Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). It is known that full-length Aβ(1-42) is more prone to aggregation than Aβ(1-40). We here search stable conformations o...
Tomoyo Kasumi, Kohta Araki, Tatsuroh Mizushima, Hiroshi Kobayashi, Noriyuki Kurita
Journal of Physics: Conference Series   433    Jan 2013
Recent biochemical experiments have elucidated that a variety of proteases play important roles in cancer invasion and metastasis. In particular, binding of urokinase-type plasminogen activator (uPA) to uPA receptor (uPAR) existing on the surface ...
A. Okamoto, K. Nomura, A. Yano, S. Higai, T. Kondo, S. Kamba, N. Kurita
Journal of Physics: Conference Series   433    Jan 2013
Aggregation of amyloid-β (Aβ) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimen...
Kazuya Nomura, Ryota Hoshino, Yasuhiro Hoshiba, Victor I. Danilov, Noriyuki Kurita
Journal of Physics: Conference Series   433    Jan 2013
We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk ...
Kazuya Nomura, Akisumi Okamoto, Atsushi Yano, Shin'Ichi Higai, Takashi Kondo, Seiji Kamba, Noriyuki Kurita
Chemical Physics Letters   547 89-96   Sep 2012   [Refereed]
Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides ...
Hirakawa T, Fujita S, Ohyama T, Dedachi K, Khan MT, Sylte I, Kurita N
Journal of molecular graphics & modelling   33 1-11   Mar 2012   [Refereed]
Yaku Maeda, Akisumi Okamoto, Yasuhiro Hoshiba, Takayuki Tsukamoto, Yasuyuki Ishikawa, Noriyuki Kurita
Computational Materials Science   53 314-320   Feb 2012   [Refereed]
The electrical conductivity of DNA duplex is affected by many factors such as DNA base sequence, hydration of DNA duplex, connecting configuration between DNA duplex and electrodes, thermal fluctuation of DNA duplex structure. We here investigate ...
Akisumi Okamoto, Yaku Maeda, Takayuki Tsukamoto, Yasuyuki Ishikawa, Noriyuki Kurita
Computational Materials Science   53 416-424   Feb 2012   [Refereed]
DNA duplexes have attracted much attention as a primary candidate for nanowires possessing self-organizing capability. To employ DNA duplexes as nanowires, however, a major drawback must be overcome; the guanine bases undergo oxidative degradation...
Yasuhiro Hoshiba, Yaku Maeda, Katsuhiro Hamada, Shouichi Fukuoka, Yasuyuki Ishikawa, Noriyuki Kurita
Chemical Physics Letters   521 39-44   Jan 2012   [Refereed]
Electrical conductivity through single molecules is affected by a variety of factors, such as solvation around the molecule, connecting configuration between the molecule and electrodes, thermal fluctuation of the molecular structure, and so on. W...
Satoshi Miyagi, Satoshi Sawamura, Eri Yoshikawa, Kenichi Dedachi, Satoshi Itoh, Mitsuko Ishihara-Sugano, Noriyuki Kurita
International Journal of Quantum Chemistry   112 289-299   Jan 2012   [Refereed]
Aryl hydrocarbon receptor (AhR) regulates expression of genes in a ligand-dependent manner. Although AhR was found to contain basic helix-loop-helix and Per-Arnt-Sim (PAS) domains, three-dimensional structures of AhR and its complex with ligand ha...
Khan MT, Mischiati C, Ather A, Ohyama T, Dedachi K, Borgatti M, Kurita N, Gambari R
Current topics in medicinal chemistry   12(8) 814-827   2012   [Refereed]
Khan MT, Dedachi K, Matsui T, Kurita N, Borgatti M, Gambari R, Sylte I
Current topics in medicinal chemistry   12(16) 1748-1762   2012   [Refereed]
KURITA NORIYUKI, ISHIKAWA YASUYUKI, DEDACHI KEN'ICHI, TSUKAMOTO TAKAYUKI
村田学術振興財団年報   (25) 91-98   Dec 2011
Kenichi Dedachi,Tatsuya Hirakawa,Seiya Fujita,Mahmud Tareq Hassan Khan,Ingebrigt Sylte,Noriyuki Kurita
Journal of Computational Chemistry   32(14) 3047-3057   Nov 2011   [Refereed]
Tsuji S, Kasumi T, Nagase K, Yoshikawa E, Kobayashi H, Kurita N
Journal of molecular graphics & modelling   29(8) 975-984   Aug 2011   [Refereed]
Tatsuya Ohyama,Masato Hayakawa,Shin Nishikawa,Noriyuki Kurita
Journal of Computational Chemistry   32(8) 1661-1670   Jun 2011   [Refereed]
Tetsumi Tanabe, Tetsumi Tanabe, Koji Noda, Satoshi Miyagi, Noriyuki Kurita, Shigenori Tanaka, Julia Setzler, Wolfgang Wenzel, Evgeni B. Starikov, Evgeni B. Starikov, Evgeni B. Starikov, Gianaurelio Cuniberti, Gianaurelio Cuniberti
Chemical Physics Letters   504 83-87   Feb 2011   [Refereed]
Electron-ion collisions were studied for various protonated peptide monocations with disulfide bonds, using an electrostatic storage-ring equipped with a merged-electron-beam device. Resonant neutral particle emissions at the energies of 6-7 eV we...
Yoshikawa E, Miyagi S, Dedachi K, Ishihara-Sugano M, Itoh S, Kurita N
Journal of molecular graphics & modelling   29(2) 197-205   Sep 2010   [Refereed]
Masato Hayakawa, Tatsuya Ohyama, Yoko Yamaguchi, Shingo Iwabuchi, Tomohiko Nakagawa, Tamie Nakajima, Noriyuki Kurita
Molecular Simulation   36 644-656   Aug 2010   [Refereed]
To elucidate the specific interactions between the peroxisome proliferator-activated receptor (PPAR) and ligand GW409544 (GW), we obtained the solvated structures of the PPAR+GW complexes for human, mouse and rat by classical molecular mechanics c...
MURAKAMI Takahiro, KURITA Noriyuki, NARUSE Ichiro
Journal of High Temperature Society   36(1) 41-46   Jan 2010   [Refereed]
Tanja van Mourik, Victor I. Danilov, Vladimir V. Dailidonis, Noriyuki Kurita, Hajime Wakabayashi, Takayuki Tsukamoto
Theoretical Chemistry Accounts   125 233-244   Jan 2010   [Refereed]
The canonical (keto) and rare (enol) tautomers of uracil and 5-bromouracil in clusters comprising 50 and 100 water molecules (nanodroplets) were studied using density functional theory. The geometries of the various complexes were optimized at two...
MURAKAMI Takahiro, KURITA Noriyuki, NARUSE Ichiro
Journal of High Temperature Society   36(1) 41-46   2010   [Refereed]
Sulfur oxides (SOx) are one of the main sources of acid rain. In a fluidized bed combustor, limestone is a directly supplied into the combustor, as a desulfurizer in order to decrease the emissions of SOx from fuel, such as s...
H. Wakabayashi, Y. Ishikawa, T. Tsukamoto, N. Kurita
ECS Transactions   16 53-64   Nov 2009   [Refereed]
To elucidate the dependence of hole transfer through DNA duplex on its base sequence, we investigated the hole transfer mechanism through the hydrated DNA duplexes with the 5′-GAGG-3′ and 5′-GTGG-3′ base sequences by ab initio molecular dynamics s...
Kenichi Dedachi, Mahmud Tareq Hassan Khan, Ingebrigt Sylte, Noriyuki Kurita
Chemical Physics Letters   479 290-295   Sep 2009   [Refereed]
Thermolysin (TLN) is a metalloprotease widely used for elaborating peptides of amino acid residues. Its enzyme activity is inhibited by the binding of dipeptide molecules. We here investigate specific interactions and binding free energies between...
Nagase K, Kobayashi H, Yoshikawa E, Kurita N
Journal of molecular graphics & modelling   28(1) 46-53   Aug 2009   [Refereed]
Takayuki Tsukamoto, Hajime Wakabayashi, Yasuo Sengoku, Noriyuki Kurita
International Journal of Quantum Chemistry   109 2058-2067   Jul 2009   [Refereed]
The dependence of charge conducting properties through DNA-duplex + Au-electrode systems on DNA base sequence, DNA conformation, structure of Au electrodes, and solvating water molecules was investigated by using molecular simulations and Green's ...
Tsukamoto T, Ishikawa Y, Sengoku Y, Kurita N
Chemical physics letters   474(4) 362-365   Jun 2009   [Refereed]
Danilov VI, van Mourik T, Kurita N, Wakabayashi H, Tsukamoto T, Hovorun DM
The journal of physical chemistry. A   113(11) 2233-2235   Mar 2009   [Refereed]
MIYAGI SATOSHI, YOSHIKAWA ERI, DEDACHI KEN'ICHI, ITO SATOSHI, ISHIHARA(SUGANO) MITSUKO, KURITA NORIYUKI
J Comput Aided Chem (Web)   10 63-75 (J-STAGE)   2009   [Refereed]
Ikuyo Komura, Yasuyuki Ishikawa, Takayuki Tsukamoto, Takayuki Natsume, Noriyuki Kurita
Journal of Molecular Structure: THEOCHEM   862 122-129   Aug 2008   [Refereed]
Stable structures of hydrated G-C and A-T base pairs and their electronic properties were investigated by density functional calculations. The results indicate that G-C and A-T pairs have drastically different patterns of hydration and that the hy...
Nakagawa T, Kurita N, Kozakai S, Iwabuchi S, Yamaguchi Y, Hayakawa M, Ito Y, Aoyama T, Nakajima T
Journal of molecular graphics & modelling   27(1) 45-58   Aug 2008   [Refereed]
Kenichi Dedachi, Yasuyuki Ishikawa, Taisuke Nakatsu, Takayuki Natsume, Takayuki Tsukamoto, Noriyuki Kurita
Journal of Molecular Structure: THEOCHEM   854 70-75   Apr 2008   [Refereed]
Structures of hydrated A-U base pair were investigated by using DFT and hybrid ONIOM methods in order to examine the efficacy of the ONIOM (QM:MM) approach in describing the structure of the hydrated RNA base pair. Comparison of these results reve...
NISHIKAWA SHIN, KOZAKAI SHINSAKU, SENGOKU YASUO, KURITA NORIYUKI
J Comput Aided Chem (Web)   9 17-29 (J-STAGE)   2008   [Refereed]
V. I. Danilov, V. U. Dailidonis, D. M. Hovorun, L. A. Zayika, N. Kurita, A. I. Potopalsky, V. M. Kharchenko
Biopolymers and Cell   23 28-34   Dec 2007   [Refereed]
The results of the extensive theoretical study on the energy and structural properties of all possible alkaloid berberine forms (berberine cation and three tautomeric forms of berberine), displaying a great variety of biological and pharmacologica...
村上 高広, 栗田 典之, 成瀬 一郎
Sulphuric acid and industry.   60(10) 177-183   Oct 2007   [Refereed]
Natsume T, Ishikawa Y, Dedachi K, Tsukamoto T, Kurita N
Chemical physics letters   446(1) 151-158   Sep 2007   [Refereed]
Tsukamoto T, Ishikawa Y, Natsume T, Dedachi K, Kurita N
Chemical physics letters   441(1-3) 136-142   Jun 2007   [Refereed]
Dedachi KI, Natsume T, Nakatsu T, Tanaka S, Ishikawa Y, Kurita N
Chemical physics letters   436(1-3) 244-251   Feb 2007   [Refereed]
Natsume T, Ishikawa Y, Dedachi K, Tsukamoto T, Kurita N
Chemical physics letters   434(1-3) 133-138   Jan 2007   [Refereed]
NAGASE KEISUKE, KOBAYASHI HIROSHI, NAGATA NOBORU, YAMAMOTO FUMIO, NATSUME TAKAYUKI, DEDACHI KEN'ICHI, TSUKAMOTO TAKAYUKI, KURITA NORIYUKI
J Comput Aided Chem (Web)   8 75-84 (J-STAGE)   2007   [Refereed]
IWABUCHI SHINGO, NAKAGAWA TOMOHIKO, NAKAMURA HARUHIKO, YAMAGUCHI YOKO, NASU TAMIE, KURITA NORIYUKI
J Comput Aided Chem (Web)   8 1-11 (J-STAGE)   2007   [Refereed]
Ewgeni B. Starikov, Ewgeni B. Starikov, Ewgeni B. Starikov, Shigenori Tanaka, Shigenori Tanaka, Noriyuki Kurita, Yasuo Sengoku, Takayuki Natsume, Aina Quintilla, Wolfgang Wenzel, Wolfgang Wenzel
Modern Methods for Theoretical Physical Chemistry of Biopolymers   535-546   Dec 2006
This chapter presents and discusses DNA conductance based upon the Kubo formula. Using this approach, the effects of base pair mismatches, different conformational changes, and base pair sequence on DNA electrical properties can be investigated. T...
Takayuki Natsume, Yasuyuki Ishikawa, Kenichi Dedachi, Takayuki Tsukamoto, Noriyuki Kurita
International Journal of Quantum Chemistry   106 3278-3287   Dec 2006   [Refereed]
The electronic properties of DNA-DNA and PNA-DNA double strands having 3-6 base pairs (bp) were investigated by density functional theory (DFT) calculations. The binding energies and the highest occupied molecular orbital-lowest unoccupied molecul...
Kenichi Dedachi, Takayuki Natsume, Taisuke Nakatsu, Yasuyuki Ishikawa, Noriyuki Kurita
International Journal of Quantum Chemistry   106 3270-3277   Dec 2006   [Refereed]
Electrochemical DNA chips determine the sequence of DNA bases by detecting the change in charge conductivity through single- or double-strand DNA. Experimentally, double-strand DNAs were found to conduct much greater electric current than single-s...
V. I. Danilov, V. V. Dailidonis, D. M. Hovorun, N. Kurita, Y. Murayama, T. Natsume, A. I. Potopalsky, L. A. Zaika
Chemical Physics Letters   430 409-413   Oct 2006   [Refereed]
The stable structures and electronic properties for the berberine cation as well as possible ammonium, carbinol and amino-aldehyde forms of protoberberine salts in the presence of hydroxyl ions were investigated by the B3LYP/6-31G(d,p) and MP2/6-3...
Takayuki Tsukamoto, Takayuki Tsukamoto, Yasuyuki Ishikawa, Marius J. Vilkas, Takayuki Natsume, Kenichi Dedachi, Noriyuki Kurita
Chemical Physics Letters   429 563-569   Oct 2006   [Refereed]
The effect of hydration on the electronic properties of DNA is investigated by density-functional calculations for the decameric 5′-d(CCATTAATGG)2-3′ DNA duplex with hydrating water molecules identified by neutron diffraction analysis. Energetical...
T. Yagyu, Y. Tsuji, S. Haruta, T. Kitanaka, Y. Yamada, R. Kawaguchi, S. Kanayama, Y. Tanase, N. Kurita, H. Kobayashi, H. Kobayashi
International Journal of Gynecological Cancer   16 1545-1551   Jul 2006   [Refereed]
The purpose of this study was to determine whether Akt and mammalian target of rapamycin (mTOR), downstream targets of phosphatidylinositol 3-kinase, are activated in endometriosis and ovarian cancer specimens. We measured total and phosphorylated...
Yagyu T, Kobayashi H, Matsuzaki H, Wakahara K, Kondo T, Kurita N, Sekino H, Inagaki K
International journal of cancer. Journal international du cancer   118(9) 2322-2328   May 2006   [Refereed]
Noriyuki Kurita, Makoto Matsuoka, Yasuo Sengoku
Journal of Theoretical and Computational Chemistry   5 59-74   Mar 2006   [Refereed]
Tetramer of lactose repressor (LacR) protein plays an essential role in controlling the transcription of DNA. The previous experimental studies elucidated that the carboxyl-terminal domain of LacR is important for the tetramerization of LacR. In t...
Takayuki Natsume, Yasuyuki Ishikawa, Ken Ichi Dedachi, Noriyuki Kurita
Chemical Physics Letters   418 239-244   Jan 2006   [Refereed]
Electronic properties of hybridized B-form DNA-DNA, PNA-DNA and PNA-PNA double strands with common base sequences were theoretically investigated by molecular orbital calculations based on the density functional theory. The computed hybridization ...
MURAKAMIKOKO, KURITATEN'YUKI, SEISEICHIRO
日本セラミックス協会学術論文誌   114(1332) 676-680 (J-STAGE)   2006   [Refereed]
IWABUCHI SHINGO, KOZAKAI SHINSAKU, KURITA NORIYUKI
J Comput Aided Chem (Web)   7 78-86 (J-STAGE)   2006   [Refereed]
Tsukamoto Takayuki, Ishikawa Yasuyuki, Natsume Takayuki, Dedachi Kenichi, Vilkas Marius J, Kurita Noriyuki
Journal of Computer Aided Chemistry   7 190-200   2006   [Refereed]
To elucidate the effect of hydration on the electronic properties of duplex DNA, we investigated the electronic properties of both dry and hydrated DNA duplexes having stacked 10 base-pairs by density functional molecular orbital (MO) calculations...
Takahashi Kiyokazu, Kurita Noriyuki
Journal of Computer Aided Chemistry   7 178-189   2006   [Refereed]
We investigated the stable structures and their electronic properties of ATP, ADP, AMP and GTP by ab initio molecular orbital calculations based on density functional theory. Furthermore, stable structures and electronic properties of Mg2+ complex...
E. B. Starikov, S. Tanaka, N. Kurita, Y. Sengoku, T. Natsume, W. Wenzel
European Physical Journal E   18 437-445   Dec 2005   [Refereed]
A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were in...
Kobayashi H, Yoshida R, Kanada Y, Fukuda Y, Yagyu T, Inagaki K, Kondo T, Kurita N, Suzuki M, Kanayama N, Terao T
Journal of periodontal research   40(6) 461-468   Dec 2005   [Refereed]
Kobayashi H, Yagyu T, Kondo T, Kurita N, Inagaki K, Haruta S, Kawaguchi R, Kitanaka T, Sakamoto Y, Yamada Y, Kanayama N, Terao T
Cancer research   65(22) 10464-10471   Nov 2005   [Refereed]
Kobayashi H, Yoshida R, Kanada Y, Fukuda Y, Yagyu T, Inagaki K, Kondo T, Kurita N, Yamada Y, Sado T, Kitanaka T, Suzuki M, Kanayama N, Terao T
Experimental dermatology   14(10) 765-774   Oct 2005   [Refereed]
Inagaki K, Kobayashi H, Yoshida R, Kanada Y, Fukuda Y, Yagyu T, Kondo T, Kurita N, Kitanaka T, Yamada Y, Sakamoto Y, Suzuki M, Kanayama N, Terao T
The Journal of biological chemistry   280(36) 31428-31437   Sep 2005   [Refereed]
Reduced syndecan-1 expression stimulates heparin-binding growth factor-mediated invasion in ovarian cancer cells in a urokinase-independent mechanism.
Matsuzaki H, Kobayashi H, Yagyu T, Wakahara K, Kondo T, Kurita N, Sekino H, Inagaki K, Suzuki M, Kanayama N, Terao T
Oncology reports   14(2) 449-457   Aug 2005   [Refereed]
Kobayashi H, Yoshida R, Kanada Y, Fukuda Y, Yagyu T, Inagaki K, Kondo T, Kurita N, Suzuki M, Kanayama N, Terao T
Journal of cancer research and clinical oncology   131(8) 527-538   Aug 2005   [Refereed]
Kobayashi H, Yoshida R, Kanada Y, Fukuda Y, Yagyu T, Inagaki K, Kondo T, Kurita N, Suzuki M, Kanayama N, Terao T
Shock (Augusta, Ga.)   23(5) 441-447   May 2005   [Refereed]
Yagyu T, Kobayashi H, Matsuzaki H, Wakahara K, Kondo T, Kurita N, Sekino H, Inagaki K, Suzuki M, Kanayama N, Terao T
The Journal of clinical endocrinology and metabolism   90(5) 3017-3021   May 2005   [Refereed]
Wakahara K, Kobayashi H, Yagyu T, Matsuzaki H, Kondo T, Kurita N, Sekino H, Inagaki K, Suzuki M, Kanayama N, Terao T
Journal of cellular biochemistry   94(5) 995-1009   Apr 2005   [Refereed]
Matsuzaki H, Kobayashi H, Yagyu T, Wakahara K, Kondo T, Kurita N, Sekino H, Inagaki K, Suzuki M, Kanayama N, Terao T
Journal of clinical oncology : official journal of the American Society of Clinical Oncology   23(7) 1463-1472   Mar 2005   [Refereed]

Misc

 
Ab Initio Study of the Minimum-energy Structure of Trans-azobenzene
Chemical Physics Letters   360,349-354    2002
"Mehcanism of Cis-to-Trans Isomerization of azobenzene: direct MD study"
J. Physical Chemistry A   107, 4555-4560    2003
Eleetronic and Li-absorption Properties of Boron and Nitrogen Substituted Graphite Sheets.
HYOUMEN   38(1) 10   2000
"Stability of Boron and Nitrogen Substituted Buckminsterfullerene,"
Trans. Mat. Res. Soc. Jpn   14B 1231-1234   1993
"Bond Energies of Diatomic Molecules and Ionization Potentials of Light Molecules Calculated by Using the Generalized Gradient Approximation,"
Computer Aided Innovation of New Materials (]G0002[), edited by M. Doyama e al. (Elsevier Science Publisshers B. V., 1993)   165   1993
Bonding and Electronic Properties of Substituted Fullerenes C58B2, C58N2 and C58 BN
Fullerene Science & Technology   1(3) 319-328   1993

Conference Activities & Talks

 
Specific interactions between retinoic acid receptor-related orphan receptor and its ligands: molecular dynamics and ab initio fragment molecular orbital calculations
Shusuke Suzuki, Syunya Nakamura, Ryosuke Saito, Kentaro Kawai, Midori Takimoto-Kamimura, Noriyuki Kurita
CBI Annual Meeting 2019   22 Oct 2019   
Determination of stable protonation states of amino acid residues in metalloproteinase-inhibitor complex: ab initio molecular simulations
Takuya Ezawa, Satoshi Sugiyama, Ayami Ara, Ingebrigt Sylte, Noriyuki Kurita
CBI Annual Meeting 2019   22 Oct 2019   
Influence of phosphorylation on structure and electronic states of tau-protein: MD and ab initio fragment MO simulations
Katsumi Suzuki, Riku Sato, Haruki Sogawa, Sergiy Shulga, Yaroslav Blume, Noriyuki Kurita
CBI Annual Meeting 2019   22 Oct 2019   
Molecular simulations on aggregation mechanism of microtubule associated Tau proteins
Riku Sato, Katsumi Suzuki, Takuya Ezawa, Shusuke Suzuki, Karpov Pavel, Sergiy Shulga, Yaroslav Blume, Noriyuki Kurita
CBI Annual Meeting 2019   22 Oct 2019   
Specific interactions between mycobacterial FtsZ and its inhibitor derivatives: molecular docking and ab initio molecular simulations
Haruki Sogawa, Shogo Tomioka, Tomoki Shinzato, Sergiy Shulga, Pavel Karpov, Yaroslav Blume, Noriyuki Kurita
CBI Annual Meeting 2018   9 Oct 2018   

Research Grants & Projects

 
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(挑戦的萌芽研究)
Project Year: 2010 - 2012    Investigator(s): Noriyuki KURITA
DNA duplexes have attracted much attention as a primary candidate for nanowires possessing self-organizing capability. To develop DNA duplexes with high electrical conductivity, several artificial nucleobases have been designed and tested in exper...
Theoretical Study on the Mechanism of Optical Energy Translation in Azodendrimer.
Grant-in-Aid for Scientific Research
Project Year: 1998 - 2006
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(B))
Project Year: 2003 - 2005    Investigator(s): Noriyuki KURITA
Electrochemical DNA chips determine the sequence of DNA bases by detecting the change in charge conductivity through single- or double-strand DNA. Experimentally, double-strand DNAs were found to conduct much greater electric current than single-s...
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research(基盤研究(B))
Project Year: 2003 - 2004    Investigator(s): Hideo SEKINO
Pair interaction approximation (Fragment Molecular Orbital Theory:FMO) is applied for developing a quantum chemical ; program system for evaluating optical property of large molecular systems. A new functional for accounting weak force such as van...
Abinitio molecular orbital calculations for DNA base stacking energy using density functional formalism.
Grant-in-Aid for Promotion of Private Scientific Research
Project Year: 1996 - 2004