Faculty Profiles - Shinoda Wataru

Papers - Shinoda Wataru

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Conformation and Orientation of Branched Acyl Chains Responsible for the Physical Stability of Diphytanoylphosphatidylcholine Reviewed International journal

Hiroshi Tsuchikawa, Takuya Ono, Masaki Yamagami, Yuichi Umegawa, Wataru Shinoda, Michio Murata

Biochemistry 59 ( 40 ) 3929 - 3938 2020.10

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})

Diphytanoylphosphatidylcholine (DPhPC) is a synthetic phospholipid in which two methyl-branched acyl chains are introduced into the glycerol moiety, mimicking phospholipids of eukaryotic and eubacterial origins. The lipid bilayers of DPhPC reproduce the outstanding physical properties of methyl-branched lipids that occur in archaeal membranes. DPhPC is commonly used as the base lipid in biophysical experiments, particularly for recording ion-channel currents. However, the dynamics of lipid molecules that induces their useful physical properties is still unclear. In this study, we examined the conformation and orientation of the methyl-branched acyl chain of DPhPC in a membrane using 2H nuclear magnetic resonance (NMR) measurements of the synthetic lipid with a high stereochemical purity and molecular dynamics (MD) simulations. Deuterium-labeled 3',3'-CD3,D-DPhPC (2) and 7',7'-CD3,D-DPhPC (3) showed the characteristic quadrupole splitting width in the 2H NMR spectra, which corresponded to the bent orientation reported for the archaeal lipid PGP-Me [Yamagami, M., et al. (2019) Biochemistry58, 3869-3879]. However, MD simulations, which reproduced the 2H NMR results well, unveiled the unknown features of DPhPC in the membrane; DPhPC has a chain-specific average orientation, where two bent orientations with upward and downward methyl groups occur at positions C3 and C7 of the sn-1 and sn-2 chains of DPhPC, respectively. These MD and NMR results reveal that these two bent orientations define the average orientation of DPhPC for the shallow part of the acyl chains, which is considered to be an important factor in the stability of DPhPC membranes.

DOI： 10.1021/acs.biochem.0c00589

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Effect of the Packing Density on the Surface Hydrophobicity of ω-Functionalized (−CF3, −CH3, −OCH3, and −OH) Self-Assembled Monolayers: A Molecular Dynamics Study Reviewed

Hari O. S. Yadav, An-Tsung Kuo, Shingo Urata, Wataru Shinoda

The Journal of Physical Chemistry C 124 ( 26 ) 14237 - 14244 2020.7

Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations Reviewed International journal

Sangjae Seo, Michio Murata, Wataru Shinoda

The Journal of Physical Chemistry Letters 11 ( 13 ) 5171 - 5176 2020.7

Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})

The asymmetric lipid composition in plasma membranes within the inner leaflet is not typically suitable for domain formation. Thus elucidation of the likelihood of the formation or stability of a raft-like domain in the inner leaflet is necessary. Herein we investigated the phase behavior of asymmetric membranes using coarse-grained molecular dynamics simulations. The lipid leaflet comprising dioleoylphosphatidylcholine (DOPC) and cholesterol (Chol) does not typically show well-developed domains in symmetric bilayer membranes; however, it does separate into liquid ordered (Lo) and liquid disordered (Ld) phases when the opposing leaflet containing sphingomyelin (SM), DOPC, and Chol demonstrates domain formation. We determine that interdigitated acyl chains modulated the partitioning of Chol in the opposing leaflet, resulting in phase separation. Similarly, the acyl chain length of SM within the opposing leaflet affected the phase behavior of the leaflet. Our results reveal the crucial role of interdigitation in determining the phase status in asymmetric membranes.

DOI： 10.1021/acs.jpclett.0c01317

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Effects of Anion on Liquid Structures of Ionic Liquids at Graphene Electrode Interface Analyzed by Molecular Dynamics Simulations Reviewed

Seiji Tsuzuki, Takenobu Nakamura, Tetsuya Morishita, Wataru Shinoda, Shiro Seki, Yasuhiro Umebayashi, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe

Batteries & Supercaps 3 ( 7 ) 658 - 667 2020.7

Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation Reviewed

Ryo Urano, Wataru Shinoda, Noriyuki Yoshii, Susumu Okazaki

The Journal of Chemical Physics 152 ( 24 ) 244115 2020.6

Property Decoupling across the Embryonic Nucleus–Melt Interface during Polymer Crystal Nucleation Reviewed

Kyle Wm. Hall, Simona Percec, Wataru Shinoda, Michael L. Klein

The Journal of Physical Chemistry B 124 ( 23 ) 4793 - 4804 2020.6

Monodisperse Polymer Melts Crystallize via Structurally Polydisperse Nanoscale Clusters: Insights from Polyethylene Reviewed

Kyle Wm. Hall, Timothy W. Sirk, Simona Percec, Michael L. Klein, Wataru Shinoda

Polymers 12 ( 2 ) 447 2020.2

pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model Reviewed

Yusuke Miyazaki, Susumu Okazaki, Wataru Shinoda

Journal of Chemical Theory and Computation 16 ( 1 ) 782 - 793 2020.1

Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation Reviewed

Kazushi Fujimoto, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki

Pure and Applied Chemistry 92 ( 10 ) 1584 - 1594 2020

Publishing type：Research paper (scientific journal)

©2020 IUPAC & De Gruyter. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. For more information, please visit: http://creativecommons.org/licenses/by-nc-nd/4.0/ 2020. Entecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two-and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-Atomistic molecular dynamic (MD) calculations. A free energy minimum of-19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum,-4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.

DOI： 10.1515/pac-2020-0109

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Molecular simulation of the shape deformation of a polymersome Reviewed

Kaushik Chakraborty, Wataru Shinoda, Sharon M. Loverde

Soft Matter 16 ( 13 ) 3234 - 3244 2020

The Amphotericin B–Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly Reviewed

Tomoya Yamamoto, Yuichi Umegawa, Hiroshi Tsuchikawa, Shinya Hanashima, Nobuaki Matsumori, Kosuke Funahashi, Sangjae Seo, Wataru Shinoda, Michio Murata

Biochemistry 58 ( 51 ) 5188 - 5196 2019.12

Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein Reviewed

Huihui Liu, Susumu Okazaki, Wataru Shinoda

Journal of Chemical Information and Modeling 59 ( 12 ) 5104 - 5110 2019.12

Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study Reviewed

Hari O. S. Yadav, An-Tsung Kuo, Shingo Urata, Wataru Shinoda

Langmuir 35 ( 44 ) 14316 - 14323 2019.11

Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers Reviewed

Kazushi Fujimoto, Rajdeep Singh Payal, Tomonori Hattori, Wataru Shinoda, Masayuki Nakagaki, Sigeyoshi Sakaki, Susumu Okazaki

Journal of Computational Chemistry 40 2571-2576 2019.11

Divining the shape of nascent polymer crystal nuclei Reviewed

Kyle Wm. Hall, Timothy W. Sirk, Simona Percec, Michael L. Klein, Wataru Shinoda

The Journal of Chemical Physics 151 ( 14 ) 144901 2019.10

Large-scale molecular dynamics simulation of perfluorosulfonic acid membranes: Remapping coarse-grained to all-atomistic simulations Reviewed

An-Tsung Kuo, Yusuke Miyazaki, Changwoon Jang, Tatsuya Miyajima, Shingo Urata, Steven O. Nielsen, Susumu Okazaki, Wataru Shinoda

Polymer 181 121766 - 121766 2019.10

tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules Reviewed

Mark Z. Griffiths, Wataru Shinoda

Journal of Chemical Information and Modeling 59 ( 9 ) 3829 - 3838 2019.9

Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes Reviewed

Masaki Yamagami, Hiroshi Tsuchikawa, Jin Cui, Yuichi Umegawa, Yusuke Miyazaki, Sangjae Seo, Wataru Shinoda, Michio Murata

Biochemistry 58 ( 37 ) 3869 - 3879 2019.9

All-atom molecular dynamics study of impact fracture of glassy polymers. I: Molecular mechanism of brittleness of PMMA and ductility of PC Reviewed

Kazushi Fujimoto, Zhiye Tang, Wataru Shinoda, Susumu Okazaki

Polymer 178 121570 - 121570 2019.9

Hydrogen Permeation in Hydrated Perfluorosulfonic Acid Polymer Membranes: Effect of Polymer Crystallinity and Equivalent Weight Reviewed

Kotono Takeuchi, An-Tsung Kuo, Takeshi Hirai, Tatsuya Miyajima, Shingo Urata, Shinji Terazono, Susumu Okazaki, Wataru Shinoda

The Journal of Physical Chemistry C 123 ( 33 ) 20628 - 20638 2019.8

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Papers - Shinoda Wataru