Yuka Ikemoto

Dr. Yuka Ikemoto


Research Focus & Metrics

Academic Career Length

33Years (1994-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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31 May 2022 in The Journal of Physical Chemistry B
Verified
Journal Article
Open access
YIYuka Ikemoto
Yuka Ikemoto
YHYoshihisa Harada
Yoshihisa Harada
Masaru TanakaMasaru Tanaka
Masaru Tanaka
SNShin-nosuke Nishimura
Shin-nosuke Nishimura
DMDaiki Murakami
Daiki Murakami
HTHajime Torii
Hajime Torii
Elucidating the state of interfacial water, especially the hydrogen-bond configurations, is considered to be key for a better understanding of the functions of polymers that are exhibited in the presence of water. Here, an analysis in this direction is conducted for two water-insoluble biocompatible polymers, poly(2-methoxyethyl acrylate) and cyclic(poly(2-methoxyethyl acrylate)), and a non-biocompatible polymer, poly(n-butyl acrylate), by measuring their IR spectra under humidified conditions and by carrying out theoretical calculations on model complex systems. It is found that the OH stretching bands of water are decomposed into four components, and while the higher-frequency components (with peaks at ∼3610 and ∼3540 cm-1) behave in parallel with the C═O and C-O-C stretching and CH deformation bands of the polymers, the lower-frequency components (with peaks at ∼3430 and ∼3260 cm-1) become pronounced to a greater extent with increasing humidity. From the theoretical calculations, it is shown that the OH stretching frequency that is distributed from ∼3650 to ∼3200 cm-1 is correlated to the hydrogen-bond configurations and is mainly controlled by the electric field that is sensed by the vibrating H atom. By combining these observed and calculated results, the configurations of water at the interface of the polymers are discussed.

17 November 2017 in Nature Communications
Verified
Journal Article
Open access
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TTTakehiko Tosha
Takehiko Tosha
TNTakashi Nomura
Takashi Nomura
TNTakuma Nishida
Takuma Nishida
NSNaoya Saeki
Naoya Saeki
KOKouta Okubayashi
Kouta Okubayashi
MKMinoru Kubo
Minoru Kubo
Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe3+-NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H− from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.

1 December 2015 in Scientific Reports
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Journal Article
Open access
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KAKatsuya Araki
Katsuya Araki
NYNaoto Yagi
Naoto Yagi
YIYuka Ikemoto
Yuka Ikemoto
HYHisashi Yagi
Hisashi Yagi
CCChi-Jing Choong
Chi-Jing Choong
HMHideki Mochizuki
Hideki Mochizuki
Lewy bodies (LBs), which mainly consist of α-synuclein (α-syn), are neuropathological hallmarks of patients with Parkinson’s disease (PD). The fine structure of LBs is unknown and LBs cannot be made artificially. Nevertheless, many studies have described fibrillisation using recombinant α-syn purified from E. coli. An extremely fundamental problem is whether the structure of LBs is the same as that of recombinant amyloid fibrils. Thus, we used synchrotron Fourier transform infrared micro-spectroscopy (FTIRM) to analyse the fine structure of LBs in the brain of PD patients. Our results showed a shift in the infrared spectrum that indicates abundance of a β-sheet-rich structure in LBs. Also, 2D infrared mapping of LBs revealed that the content of the β-sheet structure is higher in the halo than in the core and the core contains a large amount of proteins and lipids.

17 August 2017 in Langmuir
Verified
Journal Article
Open access
YHYuji Higaki
Yuji Higaki
YIYoshihiro Inutsuka
Yoshihiro Inutsuka
TSTatsunori Sakamaki
Tatsunori Sakamaki
YTYuki Terayama
Yuki Terayama
ATAi Takenaka
Ai Takenaka
Atsushi TakaharaAtsushi Takahara
Atsushi Takahara
Effect of alkyl chain spacer length between the charged groups (CSL) in zwitterionic poly(sulfobetaine) (PSB) brushes on the hydration state was investigated. PSB brushes with ethyl (PMAES), propyl (PMAPS), or butyl (PMABS) CSL were prepared by surface-initiated atom transfer radical polymerization on silicon wafers. Hydration states of the PSB brushes in aqueous solutions and/or humid vapor were investigated by contact angle measurement, infrared spectroscopy, AFM observation, and neutron reflectivity. The PSB brushes are swollen in humid air and deionized water due to the hydration of the charged groups leading to the reduction of hydrated PSB brushes/water interfacial free energy. The hydrated PSB brushes exhibit clear interface with low interfacial roughness due to networking of the PSB brush chains through association of the SBs. The hydrated PSB brushes produce diffusive swollen layer in the presence of NaCl because of the charge screening followed by SB dissociation by the bound ions. The ionic strength sensitivity in the hydration got more significant with increasing the CSL in SBs because of the augmentation in partial charge by charged group separation.

1 September 2012 in Polymer
Verified
Journal Article
Closed access
TYTakahiro Yano
Takahiro Yano
Yuji HigakiYuji Higaki
Yuji Higaki
DTDi Tao
Di Tao
DMDaiki Murakami
Daiki Murakami
MKMotoyasu Kobayashi
Motoyasu Kobayashi
Atsushi TakaharaAtsushi Takahara
Atsushi Takahara

2 June 2004 in Physical Review Letters
Verified
Journal Article
Closed access
PDF file
TSTakahiko Sasaki
Takahiko Sasaki
NYN. Yoneyama
N. Yoneyama
NKN. Kobayashi
N. Kobayashi
YIYuka Ikemoto
Yuka Ikemoto
HKH. Kimura
H. Kimura
Electronic phase separation consisting of the metallic and insulating domains with 50–100   μm in diameter is found in the organic Mott system κ−[(h8−BEDT−TTF)1−x(d8−BEDT−TTF)x]2Cu[N(CN)2]Br by means of scanning microregion infrared spectroscopy using the synchrotron radiation. The phase separation appears below the critical end temperature 35–40 K of the first-order Mott transition. The observation of the macroscopic size of the domains indicates a different class of the intrinsic electronic inhomogeneity from the nanoscale one reported in the inorganic Mott systems such as high-Tc copper and manganese oxides.