Search Results - "Kanematsu, Yusuke"

Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme by Kanematsu, Yusuke, Tachikawa, Masanori

“…Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics)…”
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Computational Exploration of Minimum Energy Reaction Pathway of N2O Formation from Intermediate I of P450nor Using an Active Center Model by Kanematsu, Yusuke, Kondo, Hiroko X., Takano, Yu

“…P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention…”
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H/D isotope effect between adsorbed water (H2O, D2O, and HDO) and H2O- and D2O-ice Ih(0 0 0 1) basal surfaces based on the combined plane wave and localized basis set method by Ishimoto, Takayoshi, Sakagami, Hiroki, Kanematsu, Yusuke, Tachikawa, Masanori

“…[Display omitted] •H/D isotope effect for adsorbed water and ice Ih(0 0 0 1) surface is analyzed.•Both surface and local parts can be adequately considered…”
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Nuclear quantum effect and H/D isotope effect in excited state intramolecular proton transfer and electron‐induced intramolecular proton transfer reactions in 8‐hydroxyquinoline by Udagawa, Taro, Hattori, Ikumi, Kanematsu, Yusuke, Ishimoto, Takayoshi, Tachikawa, Masanori

“…The optimum exponent α (αopt) value in 1s Gaussian type function (GTF) was analyzed to develop nuclear basis function for multicomponent quantum mechanics…”
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Statistical and quantum-chemical analysis of the effect of heme porphyrin distortion in heme proteins: Differences between oxidoreductases and oxygen carrier proteins by Kanematsu, Yusuke, Kondo, Hiroko X., Imada, Yasuhiro, Takano, Yu

“…[Display omitted] •Statistical and quantum-chemical analysis of heme distortion was performed.•PCA implied oxidoreductases preferred ruffling distortions to…”
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Random Forest Classifier of Heme Proteins Using Porphyrin Distortions and Axial Ligands of Heme by Fujikawa, Hinako, Kondo, Hiroko X., Kanematsu, Yusuke, Takano, Yu

“…We achieved success in the construction of a random forest classifier that is capable of accurately classifying heme proteins for oxygen storage/transport…”
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Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket by Kondo, Hiroko X, Fujii, Masanori, Tanioka, Takuma, Kanematsu, Yusuke, Yoshida, Takashi, Takano, Yu

“…Heme proteins play diverse and important biological roles, from electron transfer and chemical catalysis to oxygen transport and/or storage. Although the…”
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PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins by Kondo, Hiroko X, Kanematsu, Yusuke, Masumoto, Gen, Takano, Yu

“…Abstract Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation…”
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Hydrogen/Deuterium Transfer from Anisole to Methoxy Radicals: A Theoretical Study of a Deuterium-Labeled Drug Model by Kimura, Yuka, Kanematsu, Yusuke, Sakagami, Hiroki, Rivera Rocabado, David S, Shimazaki, Tomomi, Tachikawa, Masanori, Ishimoto, Takayoshi

“…Recently, deuterium-labeled drugs, such as deutetrabenazine, have attracted considerable attention. Consequently, understanding the reaction mechanisms of…”
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Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate by Tosha, Takehiko, Nomura, Takashi, Nishida, Takuma, Saeki, Naoya, Okubayashi, Kouta, Yamagiwa, Raika, Sugahara, Michihiro, Nakane, Takanori, Yamashita, Keitaro, Hirata, Kunio, Ueno, Go, Kimura, Tetsunari, Hisano, Tamao, Muramoto, Kazumasa, Sawai, Hitomi, Takeda, Hanae, Mizohata, Eiichi, Yamashita, Ayumi, Kanematsu, Yusuke, Takano, Yu, Nango, Eriko, Tanaka, Rie, Nureki, Osamu, Shoji, Osami, Ikemoto, Yuka, Murakami, Hironori, Owada, Shigeki, Tono, Kensuke, Yabashi, Makina, Yamamoto, Masaki, Ago, Hideo, Iwata, So, Sugimoto, Hiroshi, Shiro, Yoshitsugu, Kubo, Minoru

“…Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a…”
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Computational study of distortion effect of Fe-porphyrin found as a biological active site by Takano, Yu, Kondo, Hiroko X., Kanematsu, Yusuke, Imada, Yasuhiro

“…Fe-porphyrin is a common heme cofactor in the active sites of proteins, and plays important roles in a variety of biochemical functions. However, the origin of…”
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Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism by Hamada, Yojiro, Kanematsu, Yusuke, Tachikawa, Masanori

“…The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5′-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal…”
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Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile by Kanematsu, Yusuke, Tachikawa, Masanori, Takano, Yu

“…The short hydrogen bond between tyrosine Yz and D1‐His190 of photosystem II (PSII) was investigated using multicomponent quantum mechanics, where the quantum…”
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A computational examination of the electric-field-induced proton transfer along the interface hydrogen bond between proton donating and accepting self-assembled monolayers by Kanematsu, Yusuke, Kato, Hiroyuki S., Yoshimoto, Shinya, Ueda, Akira, Yamamoto, Susumu, Mori, Hatsumi, Yoshinobu, Jun, Matsuda, Iwao, Tachikawa, Masanori

“…[Display omitted] •We investigated the influence of electric field on hydrogen bonds by DFT calculation.•The field induced proton switching in CatTTF and…”
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Strong Hydrogen Bonds at the Interface between Proton-Donating and -Accepting Self-Assembled Monolayers on Au(111) by Kato, Hiroyuki S, Yoshimoto, Shinya, Ueda, Akira, Yamamoto, Susumu, Kanematsu, Yusuke, Tachikawa, Masanori, Mori, Hatsumi, Yoshinobu, Jun, Matsuda, Iwao

“…Hydrogen-bonding heterogeneous bilayers on substrates have been studied as a base for new functions of molecular adlayers by means of atomic force microscopy…”
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Computational analysis of H/D isotope effect on adsorption of water and its dissociated species on Pt(111) surface by Nasu, Kazuma, Sakagami, Hiroki, Kanematsu, Yusuke, Rivera Rocabado, David S., Shimazaki, Tomomi, Tachikawa, Masanori, Ishimoto, Takayoshi

“…To understand the mechanism of the H–D exchange reaction for synthesizing various deuterium-labeled molecules on heterogeneous metal catalysts as a first step,…”
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Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network by Kondo, Hiroko X, Iizuka, Hiroyuki, Masumoto, Gen, Kabaya, Yuichi, Kanematsu, Yusuke, Takano, Yu

“…Structure-function relationships in proteins have been one of the crucial scientific topics in recent research. Heme proteins have diverse and pivotal…”
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Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network by Kondo, Hiroko X, Iizuka, Hiroyuki, Masumoto, Gen, Kabaya, Yuichi, Kanematsu, Yusuke, Takano, Yu

“…Heme proteins serve diverse and pivotal biological functions. Therefore, clarifying the mechanisms of these diverse functions of heme is a crucial scientific…”
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Substrate-shielding and hydrolytic reaction in hydrolases by Kanematsu, Yusuke, Koike, Ryotaro, Amemiya, Takayuki, Ota, Motonori

“…In general, transferases undergo large structural changes and sequester substrate molecules, to shield them from water. By contrast, hydrolases exhibit only…”
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Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein by Kanematsu, Yusuke, Kamikubo, Hironari, Kataoka, Mikio, Tachikawa, Masanori

“…Photoactive yellow protein (PYP) has a characteristic hydrogen bond (H bond) between p-coumaric acid chromophore and Glu46, whose OH bond length has been…”
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