Faculty Profiles - Shinoda Wataru

Papers - Shinoda Wataru

Division display 1 - 20 of about 167 ／ All the affair displays >>

Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study. Reviewed International journal

Yuichi Umegawa, Tomoya Yamamoto, Mayank Dixit, Kosuke Funahashi, Sangjae Seo, Yasuo Nakagawa, Taiga Suzuki, Shigeru Matsuoka, Hiroshi Tsuchikawa, Shinya Hanashima, Tohru Oishi, Nobuaki Matsumori, Wataru Shinoda, Michio Murata

Science advances 8 ( 24 ) eabo2658 2022.6

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

Amphotericin B, an antifungal drug with a long history of use, forms fungicidal ion-permeable channels across cell membranes. Using solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we experimentally elucidated the three-dimensional structure of the molecular assemblies formed by this drug in membranes in the presence of the fungal sterol ergosterol. A stable assembly consisting of seven drug molecules was observed to form an ion conductive channel. The structure is somewhat similar to the upper half of the barrel-stave model proposed in the 1970s but substantially different in the number of molecules and in their arrangement. The present structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.

DOI： 10.1126/sciadv.abo2658

PubMed

researchmap

Selective adsorption of unmethylated DNA on ZnO nanowires for separation of methylated DNA Reviewed

Marina Musa, Zetao Zhu, Hiromi Takahashi, Wataru Shinoda, Yoshinobu Baba, Takao Yasui

Lab on a Chip 25 ( 7 ) 1637 - 1646 2025.4

Asymmetry and Heterogeneity in the Plasma Membrane

Teppei Yamada, Wataru Shinoda

2025.3

Publisher：Cold Spring Harbor Laboratory

Plasma membranes (PMs) exhibit asymmetry between their two leaflets in terms of phospholipid headgroups, unsaturation, and resulting membrane properties such as packing and fluidity. Lateral heterogeneity, including the formation of lipid domains, is another crucial aspect of PMs with significant biological implications. However, the nature and even the existence of lipid domains in the two leaflets of PMs remain elusive, hindering a complete understanding of the significance of lipid asymmetry. Using coarse-grained molecular dynamics simulation of the asymmetric PM, we find that the outer leaflet predominantly adopts a liquid-ordered state, whereas the inner leaflet separates into nanoscale (≈10 nm) liquid-ordered and liquid-disordered domains, exhibiting highly dynamic fusion and fission events. This structural asymmetry is further reinforced by asymmetric lateral stress resulting from a cholesterol bias toward the outer leaflet. These findings suggest distinct functional roles for the two leaflets, modulated by asymmetric lateral stress. Additionally, comparing the phase behavior of asymmetric and fully scrambled PMs reveals a key determinant of domain size: intact PMs maintain nanoscale domains, while cell-derived giant PM vesicles, which have lost the strict lipid asymmetry, exhibit microscale domains.

DOI： 10.1101/2025.03.03.641122

researchmap

NMR and molecular simulation studies on the structure elucidation of the amphotericin B ion channel using 13C and 19F labelling Invited Reviewed

Yuichi Umegawa, Hiroshi Tsuchikawa, Wataru Shinoda, Michio Murata

Organic & Biomolecular Chemistry 2025

Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation Reviewed

Kevin A. Alberto, M. N. Hasna Begam, Hejian Xiong, Wataru Shinoda, Paul A. Slesinger, Zhenpeng Qin, Steven O. Nielsen

Nanoscale 2025

Linear ether-based highly concentrated electrolytes for Li–sulfur batteries Reviewed

Toru Ishikawa, Shohei Haga, Keisuke Shigenobu, Taku Sudoh, Seiji Tsuzuki, Wataru Shinoda, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno

Faraday Discussions 253 385 - 406 2024.10

Evolving better solvate electrolytes for lithium secondary batteries Reviewed International coauthorship International journal

Frederik Philippi, Maleen Middendorf, Keisuke Shigenobu, Yuna Matsuyama, Oriele Palumbo, David Pugh, Taku Sudoh, Kaoru Dokko, Masayoshi Watanabe, Monika Schönhoff, Wataru Shinoda, Kazuhide Ueno

Chemical Science 15 ( 19 ) 7342 - 7358 2024.4

Publishing type：Research paper (scientific journal)

The overall performance of lithium batteries remains unmatched to this date. Decades of optimisation have resulted in long-lasting batteries with high energy density suitable for mobile applications. However, the electrolytes used at present suffer from low lithium transference numbers, which induces concentration polarisation and reduces efficiency of charging and discharging. Here we show how targeted modifications can be used to systematically evolve anion structural motifs which can yield electrolytes with high transference numbers. Using a multidisciplinary combination of theoretical and experimental approaches, we screened a large number of anions. Thus, we identified anions which reach lithium transference numbers around 0.9, surpassing conventional electrolytes. Specifically, we find that nitrile groups have a coordination tendency similar to SO2 and are capable of inducing the formation of Li+ rich clusters. In the bigger picture, we identified a balanced anion/solvent coordination tendency as one of the key design parameters.

DOI： 10.1039/d4sc01492h

Scopus

researchmap

Discrimination of extracellular miRNA sources for the identification of tumor-related functions based on nanowire thermofluidics Reviewed

Kunanon Chattrairat, Akira Yokoi, Min Zhang, Mikiko Iida, Kosuke Yoshida, Masami Kitagawa, Ayuka Niwa, Masatoshi Maeki, Takeshi Hasegawa, Takeshi Yokoyama, Yoshikazu Tanaka, Yusuke Miyazaki, Wataru Shinoda, Manabu Tokeshi, Kazuki Nagashima, Takeshi Yanagida, Hiroaki Kajiyama, Yoshinobu Baba, Takao Yasui

Device 12 100363 - 100363 2024.4

Light-controllable cell-membrane disturbance for intracellular delivery. Reviewed International journal

Wenting Huo, Koji Miki, Huiying Mu, Takashi Osawa, Harumi Yamaguma, Yuuya Kasahara, Satoshi Obika, Yoshimasa Kawaguchi, Hisaaki Hirose, Shiroh Futaki, Yusuke Miyazaki, Wataru Shinoda, Shuji Akai, Kouichi Ohe

Journal of Materials Chemistry. B 12 ( 17 ) 4138 - 4147 2024.3

Language：English Publishing type：Research paper (scientific journal)

Highly polar and charged molecules, such as oligonucleotides, face significant barriers in crossing the cell membrane to access the cytoplasm. To address this problem, we developed a light-triggered twistable tetraphenylethene (TPE) derivative, TPE-C-N, to facilitate the intracellular delivery of charged molecules through an endocytosis-independent pathway. The central double bond of TPE in TPE-C-N is planar in the ground state but becomes twisted in the excited state. Under light irradiation, this planar-to-twisted structural change induces continuous cell membrane disturbances. Such disturbance does not lead to permanent damage to the cell membrane. TPE-C-N significantly enhanced the intracellular delivery of negatively charged molecules under light irradiation when endocytosis was inhibited through low-temperature treatment, confirming the endocytosis-independent nature of this delivery method. We have successfully demonstrated that the TPE-C-N-mediated light-controllable method can efficiently promote the intracellular delivery of charged molecules, such as peptides and oligonucleotides, with molecular weights ranging from 1000 to 5000 Da.

DOI： 10.1039/d3tb02956e

PubMed

researchmap

Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin. Reviewed International journal

Yuichi Umegawa, Sho Kato, Sangjae Seo, Wataru Shinoda, Satoshi Kawatake, Shigeru Matsuoka, Michio Murata

Biophysical chemistry 308 107204 - 107204 2024.2

Language：English Publishing type：Research paper (scientific journal)

Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.

DOI： 10.1016/j.bpc.2024.107204

PubMed

researchmap

pSPICA Force Field Extended for Proteins and Peptides Reviewed

Yusuke Miyazaki, Wataru Shinoda

Journal of Chemical Information and Modeling 64 ( 2 ) 532 - 542 2024.1

Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations Reviewed International journal

Masatoshi Maeki, Niko Kimura, Yuto Okada, Kazuki Shimizu, Kana Shibata, Yusuke Miyazaki, Akihiko Ishida, Kento Yonezawa, Nobutaka Shimizu, Wataru Shinoda, Manabu Tokeshi

Nanoscale Advances 6 ( 8 ) 2166 - 2176 2024

Molecular Level Origin of Ion Dynamics in Highly Concentrated Electrolytes Invited Reviewed

Keisuke Shigenobu, Seiji Tsuzuki, Frederik Philippi, Taku Sudoh, Yosuke Ugata, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno, Wataru Shinoda

The Journal of Physical Chemistry B 127 ( 48 ) 10422 - 10433 2023.12

Improved Protein Model in SPICA Force Field Reviewed

Teppei Yamada, Yusuke Miyazaki, Shogo Harada, Ashutosh Kumar, Stefano Vanni, Wataru Shinoda

Journal of Chemical Theory and Computation 19 ( 23 ) 8967 - 8977 2023.11

Pragmatic Coarse-Graining of Proteins: Models and Applications Reviewed

Luís Borges-Araújo, Ilias Patmanidis, Akhil P. Singh, Lucianna H. S. Santos, Adam K. Sieradzan, Stefano Vanni, Cezary Czaplewski, Sergio Pantano, Wataru Shinoda, Luca Monticelli, Adam Liwo, Siewert J. Marrink, Paulo C. T. Souza

Journal of Chemical Theory and Computation 19 ( 20 ) 7112 - 7135 2023.10

HER-2-targeted Boron Neutron Capture Therapy with Carborane-integrated Immunoliposomes Prepared via an Exchanging Reaction. Reviewed International journal

Riku Kawasaki, Ayano Oshige, Keita Yamana, Hidetoshi Hirano, Kotaro Nishimura, Yamato Miura, Ryuji Yorioka, Yu Sanada, Kaori Bando, Anri Tabata, Kazuma Yasuhara, Yusuke Miyazaki, Wataru Shinoda, Tomoki Nishimura, Hideki Azuma, Takushi Takata, Yoshinori Sakurai, Hiroki Tanaka, Minoru Suzuki, Takeshi Nagasaki, Atsushi Ikeda

Chemistry (Weinheim an der Bergstrasse, Germany) 29 ( 72 ) e202302486 2023.10

Language：English Publishing type：Research paper (scientific journal)

Boron neutron capture therapy (BNCT) is a promising modality for cancer treatment because of its minimal invasiveness. To maximize the therapeutic benefits of BNCT, the development of efficient platforms for the delivery of boron agents is indispensable. Here, we prepared carborane-integrated immunoliposomes via an exchanging reaction to achieve HER-2-targeted BNCT. The conjugation of an anti-HER-2 antibody to carborane-integrated liposomes successfully endowed these liposome with targeting properties toward HER-2-overexpressing human ovarian cancer cells (SK-OV3); the resulting BNCT activity toward SK-OV3 cells obtained using the current immunoliposomal system was 14-fold that of the l-BPA/fructose complex, which is a clinically available boron agent. Moreover, the growth of spheroids treated with our system followed by thermal neutron irradiation was significantly suppressed compared with treatment with the l-BPA/fructose complex.

DOI： 10.1002/chem.202302486

PubMed

researchmap

Elucidation of Ion Channel Structure and Mechanism of Action of Amphotericin B, an Antifungal Agent Invited Reviewed

Yuichi UMEGAWA, Wataru SHINODA, Michio MURATA

KAGAKU TO SEIBUTSU 61 ( 9 ) 419 - 431 2023.9

Complex Energy Landscapes of Self-Assembled Vesicles Reviewed

Jiabin Luan, Danni Wang, Shaohua Zhang, Yusuke Miyazaki, Wataru Shinoda, Daniela A. Wilson

Journal of the American Chemical Society 145 ( 28 ) 15496 - 15506 2023.7

Molecular Dynamics Simulations of High-Concentration Li[TFSA] Sulfone Solution: Effect of Easy Conformation Change of Sulfolane on Fast Diffusion of Li Ion Invited Reviewed

Seiji Tsuzuki, Shuhei Ikeda, Wataru Shinoda, Keisuke Shigenobu, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe

JOURNAL OF PHYSICAL CHEMISTRY B 127 ( 28 ) 6333 - 6341 2023.7

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

The parameters of the polarizableforce field used formoleculardynamics simulations of Li diffusion in high-concentration lithiumbis(trifluoro-methanesulfonyl)-amide (Li[TFSA]) sulfone(sulfolane, dimethylsulfone, ethylmethylsulfone, and ethyl-i-propylsulfone) solutions were refined. The densities ofthe solutions obtained by molecular dynamics simulations reproducedwell the experimental values. The calculated concentration, temperature,and solvent dependencies of self-diffusion coefficients of ions andsolvents in the mixtures well reproduce the experimentally observeddependencies. Ab initio calculations show that theintermolecular interactions between Li ions and four sulfones arenot largely different. Conformational analyses show that sulfolanecan change the conformation more easily owing to lower barrier heightfor pseudorotation compared to the rotational barrier heights of diethylsulfoneand ethylmethylsulfone. Molecular dynamics simulations indicate thatthe easy conformation change of solvent affects the rotational relaxationof the solvent and the diffusion of Li ion in the mixture. The easyconformation change of sulfolane is one of the causes of faster diffusionof Li ion in the mixture of Li[TFSA] and sulfolane compared to themixtures of smaller dimethylsulfone and ethylmethylsulfone.

DOI： 10.1021/acs.jpcb.3c02009

Web of Science

researchmap

Lithium-Ion Dynamics in Sulfolane-Based Highly Concentrated Electrolytes Invited Reviewed

Shuhei Ikeda, Seiji Tsuzuki, Taku Sudoh, Keisuke Shigenobu, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe, Wataru Shinoda

JOURNAL OF PHYSICAL CHEMISTRY C 127 ( 28 ) 13837 - 13845 2023.7

Authorship：Last author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Here,we report the use of molecular dynamics simulationswitha polarizable force field to investigate Li-ion dynamics in sulfolane(SL)-based electrolytes. In SL-based highly concentrated electrolytes(HCEs) (e.g., SL/Li = 2:1), Li displays faster translational motionthan other components, which should be related to the structural anddynamical properties of SL. In HCEs, a transient conduction networkthat penetrated the simulation system was always observed. Rapid (<1ns) Li-ion hopping between adjacent coordination sites was observedthroughout the network. Additionally, SLs rotated in the same timeframewithout disrupting the conduction network. This rotation is believedto promote the hopping diffusion in the network. This was followedby a rotational relaxation of the SL dipole axis around the non-polarcyclohydrocarbon segment of SL (& SIM;3.3 ns), which involves areorganization of the network structure and an enhancement of thetranslational motion of the coordinating Li ions. The observed lifetimeof Li-SL coordination was longer (>11 ns). Hence, it wasconcludedthat the faster Li translational motion was obtained due to the fasterrotational relaxation time of SL rather than the lifetime of Li-SLbinding. The faster rotation of SL is related to its amphiphilic molecularstructure with compact non-polar segments. Transport properties, suchas the Onsager transport coefficients, ionic conductivity, and transferencenumber under anion-blocking conditions, were also analyzed to characterizethe features of the SL-based electrolyte.

DOI： 10.1021/acs.jpcc.3c02155

Web of Science

researchmap

　 PREV - NEXT 　

< Shinoda Wataru >

Papers - Shinoda Wataru