Search Results - "Yoneda, Shigetaka"

Potential of mean force and umbrella sampling simulation for the transport of 5‐oxazolidinone in heterotetrameric sarcosine oxidase by Yoneda, Shigetaka, Saito, Takami, Nakajima, Daisuke, Watanabe, Go

“…The structure of heterotetrameric sarcosine oxidase (HSO) contains a highly complex system composed of a large cavity and tunnels, which are essential for the…”
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Molecular Dynamics Simulations to Determine the Structure and Dynamics of Hepatitis B Virus Capsid Bound to a Novel Anti-viral Drug by Watanabe, Go, Sato, Shunsuke, Iwadate, Mitsuo, Umeyama, Hideaki, Hayakawa, Michiyo, Murakami, Yoshiki, Yoneda, Shigetaka

“…Hepatitis B virus (HBV) chronically infects millions of people worldwide and is a major cause of serious liver diseases, including liver cirrhosis and liver…”
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Parallel Evolution of Two dmrt1-Derived Genes, dmy and dm-W, for Vertebrate Sex Determination by Ogita, Yusaku, Mawaribuchi, Shuuji, Nakasako, Kei, Tamura, Kei, Matsuda, Masaru, Katsumura, Takafumi, Oota, Hiroki, Watanabe, Go, Yoneda, Shigetaka, Takamatsu, Nobuhiko, Ito, Michihiko

“…Animal sex-determining genes, which bifurcate for female and male development, are diversified even among closely related species. Most of these genes emerged…”
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CAPLIB: A New Program Library for the Modeling and Analysis of Icosahedrally Symmetric Viral Capsids by Yoneda, Shigetaka, Hara-Yamada, Yukina, Kosugi, Aya, Nanao, Maiko, Saito, Takami, Sato, Shunsuke, Yamada, Nozomu, Watanabe, Go

“…A new program library named “CAPLIB” was developed for the modeling and analysis of icosahedrally symmetric virus capsids. CAPLIB is equipped with the…”
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Structure and dynamics of the GH loop of the foot-and-mouth disease virus capsid by Azuma, Hiroko, Yoneda, Shigetaka

“…The GH loop of VP1 of the foot-and-mouth disease virus capsid is important because it is a major antigenic site and an integrin recognition site. The GH loop…”
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Analysis of Low-Frequency Phonons in Guanosine Dihydrate Based on Molecular Dynamics Simulations by Yoneda, Shigetaka, Sugawara, Yoko, Urabe, Hisako

“…Fourier analysis, using the atomic trajectory calculated by molecular dynamics simulation at 300 K, is applied to the study of low-frequency phonons of guanine…”
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Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase by Watanabe, Go, Nakajima, Daisuke, Hiroshima, Akinori, Suzuki, Haruo, Yoneda, Shigetaka

“…A precise 100-ns molecular dynamics simulation in aquo was performed for the heterotetrameric sarcosine oxidase bound with a substrate analogue,…”
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Molecular dynamics study on the hydrogen bond formation between α-hydrogen atom of L-Phe and N5 atom of FAD in the enzyme-substrate complex of the L-Phe oxidase reaction by Suzuki, Haruo, Ootaki, Masanori, Yoneda, Shigetaka

“…It is difficult to observe the structure of the enzyme-substrate complex (ES complex) experimentally, since the complex changes to the enzyme and its product…”
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Crystal Water Dynamics of Guanosine Dihydrate:  Analysis of Atomic Displacement Parameters, Time Profile of Hydrogen-Bonding Probability, and Translocation of Water by MD Simulation by Yoneda, Shigetaka, Sugawara, Yoko, Urabe, Hisako

“…The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed…”
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A Further Implementation of the Rotational Symmetry Boundary Conditions for Calculations of P43212 Symmetry Crystals by Yoneda, Shigetaka

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Dynamic Characteristics of a Peptide-Binding Groove of Human HLA-A2 Class I MHC Molecules: Normal Mode Analysis of the Antigen Peptide–Class I MHC Complex by Nojima, Hiroyuki, Takeda-Shitaka, Mayuko, Kurihara, Youji, Adachi, Masaaki, Yoneda, Shigetaka, Kamiya, Kenshu, Umeyama, Hideaki

“…Class I major histocompatibility complex (MHC) binds antigen peptides with various sequences. We performed a normal mode analysis of HLA-A2 MHC that binds…”
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Comprehensive Understanding of Host- and Guest-Dependent Helix Inversion in Chiral Nematic Liquid Crystals: Experimental and Molecular Dynamics Simulation Study by Yoshida, Jun, Tamura, Syuhei, Hoshino, Keisuke, Yuge, Hidetaka, Sato, Hisako, Yamazaki, Akane, Yoneda, Shigetaka, Watanabe, Go

“…Nematic liquid crystals (LCs) are known to transform into chiral nematic LCs with helical structures upon doping with enantiomeric compounds (called chiral…”
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Further Developement of Rotational Symmetry Boundary Condition: Simulation of Pentamer in Icosahedrally Symmetric Virus Capsid by Yoneda, Shigetaka, Nanao, Maiko

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Motion of an antiviral compound in a rhinovirus capsid under rotational symmetry boundary conditions by Yoneda, Shigetaka, Yoneda, Teruyo, Kurihara, Youji, Umeyama, Hideaki

“…A molecular dynamics (MD) simulation of a complex of a rhinovirus protein shell referred to as a “capsid” and an anti-rhinovirus drug, WIN52084s, was performed…”
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Roles of the aromatic residues conserved in the active center of Saccharomycopsis .alpha.-amylase for transglycosylation and hydrolysis activity by Matsui, Ikuo, Yoneda, Shigetaka, Ishikawa, Kazuhiko, Miyairi, Sachio, Fukui, Sakuzo, Umeyama, Hideaki, Honda, Koichi

“…The molecular structure of saccharomycopsis fibuligera alpha-amylase was predicted by a homology based modeling technique, and the amino acid residues…”
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Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions by Yoneda, Shigetaka, Kitazawa, Masako, Umeyama, Hideaki

“…The rotational symmetry boundary condition proposed by Cagin et al. [J. Comp. Chem., 12, 627 (1991)] is implemented in the molecular dynamics simulation…”
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A homology modeling method of an icosahedral viral capsid: inclusion of surrounding protein structures by Yoneda, Teruyo, Yoneda, Shigetaka, Takayama, Naoko, Kitazawa, Masako, Umeyama, Hideaki

“…A methodological development is presented for homology modeling of an icosahedrally symmetric assembly of proteins. In the method, a main-chain structure of an…”
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Intermediate state during the crystal transition in aspartame, studied with thermal analysis, solid-state NMR, and molecular dynamics simulation by EBISAWA, K, NAGASHIMA, N, FUKUHARA, K.-I, KUMON, S, KISHIMOTO, S.-I, SUZUKI, E.-I, YONEDA, S, UMEYAMA, H

“…Aspartame (L-alpha-aspartyl-L-phenylalanine methyl ester) is a dipeptide sweetener about 200 times as sweet as sugar. It exists in crystal forms such as IA,…”
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Importance of folded monomer and extended antiparallel dimer structures as enkephalin active conformation Molecular dynamics simulations of [Met 5]enkephalin in water by Yoneda, Shigetaka, Kitamura, Kunihiro, Doi, Mitsunobu, Inoue, Masatoshi, Ishida, Toshimasa

“…Simulations of the molecular dynamics of the [Met 5]enkephalin monomer and dimer structures in water have been carried out. The dynamic trajectories have been…”
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Induced fitting between a complex of four nucleotides and the cognate amino acid by Yoneda, S, Shimizu, M, Fujii, S, Go, N

“…The conformation of the hydrogen-bonded complex of a trinucleoside diphosphate (anticodon bases), a nucleic acid base (discriminator base), and an amino acid…”
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