2021/10/23 更新

写真b

ヤマダ ヤスユキ
山田 康之
YAMADA Yasuyuki
*大学が定期的に情報更新している項目(その他は、researchmapの登録情報を転載)
所属*
理学部 生命理学科
理学研究科 生命理学専攻博士課程後期課程
理学研究科 生命理学専攻博士課程前期課程
職名*
教授
学位
博士(理学) ( 1999年3月   東京工業大学 ) / 修士(理学) ( 1996年3月   東京工業大学 )
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研究テーマ*
  • タンパク質の構造変化がどのように機能に影響するかを明らかにする。主にFoF1-ATP合成酵素を材料として、その活性調節の分子機構を生物物理学的手法、生化学的手法により研究している。ATP合成酵素の調節サブユニットがどのような変化をすることで、ATP合成酵素複合体の活性をどのように制御しているかを、分子レベルで理解することをめざしている。

  • 研究キーワード
  • allosteric

  • 活性調節

  • ATP合成酵素

  • 学内職務経歴*
    • 2015年4月 - 現在 
      理学部   生命理学科   教授
    • 2015年4月 - 現在 
      理学研究科   生命理学専攻博士課程前期課程   教授
    • 2015年4月 - 現在 
      理学研究科   生命理学専攻博士課程後期課程   教授
    • 2014年4月 - 2015年3月 
      理学研究科   生命理学専攻博士課程後期課程   准教授
    • 2013年4月 - 2014年3月 
      理学研究科   生命理学専攻博士課程前期課程   准教授
    • 2008年4月 - 2015年3月 
      理学部   生命理学科   准教授
    • 2004年4月 - 2008年3月 
      理学部   生命理学科   専任講師
     

    研究分野

    • ライフサイエンス / 生物物理学

    • ライフサイエンス / 機能生物化学

    経歴

    • 2015年4月 - 現在 
      立教大学   理学部 生命理学科   教授

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    • 2008年4月 - 2015年3月 
      立教大学   理学部 生命理学科   准教授

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    • 2004年4月 - 2008年3月 
      立教大学   理学部 生命理学科   専任講師

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    • 2003年4月 - 2004年3月 
      東京大学 生産技術研究所   産学官連携研究員

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    • 1999年4月 - 2003年3月 
      日本学術振興会   特別研究員(PD)

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    • 1998年4月 - 1999年3月 
      日本学術振興会   特別研究員(DC2)

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    ▼全件表示

    学歴

    • 1996年4月 - 1999年3月 
      東京工業大学   生命理工学研究科   バイオサイエンス専攻

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      国名: 日本国

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    • 1994年4月 - 1996年3月 
      東京工業大学   生命理工学研究科   バイオサイエンス専攻

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      国名: 日本国

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    • 1990年4月 - 1994年3月 
      東京工業大学   生命理工学部   生命理学科

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      国名: 日本国

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    受賞

    • 2008年10月  
      日本生化学会  平成20年度 日本生化学会奨励賞 
       
      山田 康之

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      受賞区分:国内学会・会議・シンポジウム等の賞 

      受賞国:日本国

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    論文

    • Evolution of Ribosomal Protein S14 Demonstrated by the Reconstruction of Chimeric Ribosomes in Bacillus subtilis. 査読有り 国際誌

      Genki Akanuma, Fujio Kawamura, Satoru Watanabe, Masaki Watanabe, Fumiya Okawa, Yousuke Natori, Hideaki Nanamiya, Kei Asai, Taku Chibazakura, Hirofumi Yoshikawa, Akiko Soma, Takashi Hishida, Yasuyuki Kato-Yamada

      Journal of bacteriology203 ( 10 )   2021年4月21日

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      担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      Ribosomal protein S14 can be classified into three types. The first, the C+ type has a Zn2+ binding motif and is ancestral. The second and third are the C- short and C- long types, neither of which contain a Zn2+ binding motif and which are ca. 90 residues and 100 residues in length, respectively. In the present study, the C+ type S14 from Bacillus subtilis ribosomes (S14BsC+) were completely replaced by the heterologous C- long type of S14 from Escherichia coli (S14Ec) or Synechococcus elongatus (S14Se). Surprisingly, S14Ec and S14Se were incorporated fully into 70S ribosomes in B. subtilis However, the growth rates as well as the sporulation efficiency of the mutants harboring heterologous S14 were significantly decreased. In these mutants, the polysome fraction was decreased and the 30S and 50S subunits accumulated unusually, indicating that cellular translational activity of these mutants was decreased. In vitro analysis showed a reduction in the translational activity of the 70S ribosome fraction purified from these mutants. The abundance of ribosomal proteins S2 and S3 in the 30S fraction in these mutants was reduced while that of S14 was not significantly decreased. It seems likely that binding of heterologous S14 changes the structure of the 30S subunit, which causes a decrease in the assembly efficiency of S2 and S3, which are located near the binding site of S14. Moreover, we found that S3 from S. elongatus cannot function in B. subtilis unless S14Se is present.IMPORTANCE S14, an essential ribosomal protein, may have evolved to adapt bacteria to zinc-limited environments by replacement of a zinc-binding motif with a zinc-independent sequence. It was expected that the bacterial ribosome would be tolerant to replacement of S14 because of the previous prediction that the spread of C- type S14 involved horizontal gene transfer. In this study, we completely replaced the C+ type of S14 in B. subtilis ribosome with the heterologous C- long type of S14 and characterized the resulting chimeric ribosomes. Our results suggest that the B. subtilis ribosome is permissive for the replacement of S14, but coevolution of S3 might be required to utilize the C- long type of S14 more effectively.

      DOI: 10.1128/JB.00599-20

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    • ATP-binding affinity of the ε subunit of thermophilic F1-ATPase under label-free conditions. 査読有り 国際誌

      Miria Fujiwara, Yasuyuki Kato-Yamada

      Biochemistry and biophysics reports21   100725 - 100725   2020年3月

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      The ε subunits of several bacterial F1-ATPases bind ATP. ATP binding to the ε subunit has been shown to be involved in the regulation of F1-ATPase from thermophilic Bacillus sp. PS3 (TF1). We previously reported that the dissociation constant for ATP of wild-type ε subunit of TF1 at 25 °C is 4.3 μM by measuring changes in the fluorescence of the dye attached to the ε subunit (Kato, S. et al. (2007) J. Biol. Chem. 282, 37618). However, we have recently noticed that this varies with the dye used. In this report, to determine the affinity for ATP under label-free conditions, we have measured the competitive displacement of 2'(3')-O-N'-methylaniloyl-aminoadenosine-5'-triphosphate (Mant-ATP), a fluorescent analog of ATP, by ATP. The dissociation constant for ATP of wild-type ε subunit of TF1 at 25 °C was determined to be 0.29 μM, which is one order of magnitude higher affinity than previously reported values.

      DOI: 10.1016/j.bbrep.2020.100725

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    • C-terminal regulatory domain of the ε subunit of Fo F1 ATP synthase enhances the ATP-dependent H+ pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis. 査読有り 国際誌

      Genki Akanuma, Tomoaki Tagana, Maho Sawada, Shota Suzuki, Tomohiro Shimada, Kan Tanaka, Fujio Kawamura, Yasuyuki Kato-Yamada

      MicrobiologyOpen8 ( 8 ) e00815   2019年8月

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      The ε subunit of Fo F1 -ATPase/synthase (Fo F1 ) plays a crucial role in regulating Fo F1 activity. To understand the physiological significance of the ε subunit-mediated regulation of Fo F1 in Bacillus subtilis, we constructed and characterized a mutant harboring a deletion in the C-terminal regulatory domain of the ε subunit (ε∆C ). Analyses using inverted membrane vesicles revealed that the ε∆C mutation decreased ATPase activity and the ATP-dependent H+ -pumping activity of Fo F1 . To enhance the effects of ε∆C mutation, this mutation was introduced into a ∆rrn8 strain harboring only two of the 10 rrn (rRNA) operons (∆rrn8 ε∆C mutant strain). Interestingly, growth of the ∆rrn8 ε∆C mutant stalled at late-exponential phase. During the stalled growth phase, the membrane potential of the ∆rrn8 ε∆C mutant cells was significantly reduced, which led to a decrease in the cellular level of 70S ribosomes. The growth stalling was suppressed by adding glucose into the culture medium. Our findings suggest that the C-terminal region of the ε subunit is important for alleviating the temporal reduction in the membrane potential, by enhancing the ATP-dependent H+ -pumping activity of Fo F1 .

      DOI: 10.1002/mbo3.815

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    • Magnesium Suppresses Defects in the Formation of 70S Ribosomes as Well as in Sporulation Caused by Lack of Several Individual Ribosomal Proteins. 査読有り 国際誌

      Genki Akanuma, Kotaro Yamazaki, Yuma Yagishi, Yuka Iizuka, Morio Ishizuka, Fujio Kawamura, Yasuyuki Kato-Yamada

      Journal of bacteriology200 ( 18 )   2018年9月15日

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      担当区分:最終著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      Individually, the ribosomal proteins L1, L23, L36, and S6 are not essential for cell proliferation of Bacillus subtilis, but the absence of any one of these ribosomal proteins causes a defect in the formation of the 70S ribosomes and a reduced growth rate. In mutant strains individually lacking these ribosomal proteins, the cellular Mg2+ content was significantly reduced. The deletion of YhdP, an exporter of Mg2+, and overexpression of MgtE, the main importer of Mg2+, increased the cellular Mg2+ content and restored the formation of 70S ribosomes in these mutants. The increase in the cellular Mg2+ content improved the growth rate and the cellular translational activity of the ΔrplA (L1) and the ΔrplW (L23) mutants but did not restore those of the ΔrpmJ (L36) and the ΔrpsF (S6) mutants. The lack of L1 caused a decrease in the production of Spo0A, the master regulator of sporulation, resulting in a decreased sporulation frequency. However, deletion of yhdP and overexpression of mgtE increased the production of Spo0A and partially restored the sporulation frequency in the ΔrplA (L1) mutant. These results indicate that Mg2+ can partly complement the function of several ribosomal proteins, probably by stabilizing the conformation of the ribosome.IMPORTANCE We previously reported that an increase in cellular Mg2+ content can suppress defects in 70S ribosome formation and growth rate caused by the absence of ribosomal protein L34. In the present study, we demonstrated that, even in mutants lacking individual ribosomal proteins other than L34 (L1, L23, L36, and S6), an increase in the cellular Mg2+ content could restore 70S ribosome formation. Moreover, the defect in sporulation caused by the absence of L1 was also suppressed by an increase in the cellular Mg2+ content. These findings indicate that at least part of the function of these ribosomal proteins can be complemented by Mg2+, which is essential for all living cells.

      DOI: 10.1128/JB.00212-18

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    • Mechanistic Insights into the Activation of Soluble Guanylate Cyclase by Carbon Monoxide: A Multistep Mechanism Proposed for the BAY 41-2272 Induced Formation of 5-Coordinate CO-Heme. 査読有り 国際誌

      Ryu Makino, Yuji Obata, Motonari Tsubaki, Tetsutaro Iizuka, Yuki Hamajima, Yasuyuki Kato-Yamada, Keisuke Mashima, Yoshitsugu Shiro

      Biochemistry57 ( 10 ) 1620 - 1631   2018年3月13日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      Soluble guanylate cyclase (sGC) is a heme-containing enzyme that catalyzes cGMP production upon sensing NO. While the CO adduct, sGC-CO, is much less active, the allosteric regulator BAY 41-2272 stimulates the cGMP productivity to the same extent as that of sGC-NO. The stimulatory effect has been thought to be likely associated with Fe-His bond cleavage leading to 5-coordinate CO-heme, but the detailed mechanism remains unresolved. In this study, we examined the mechanism under the condition including BAY 41-2272, 2'-deoxy-3'-GMP and foscarnet. The addition of these effectors caused the original 6-coordinate CO-heme to convert to an end product that was an equimolar mixture of a 5- and a new 6-coordinate CO-heme, as assessed by IR spectral measurements. The two types of CO-hemes in the end product were further confirmed by CO dissociation kinetics. Stopped-flow measurements under the condition indicated that the ferrous sGC bound CO as two reversible steps, where the primary step was assigned to the full conversion of the ferrous enzyme to the 6-coordinate CO-heme, and subsequently followed by the slower second step leading a partial conversion of the 6-coordinate CO-heme to the 5-coordinate CO-heme. The observed rates for both steps linearly depended on CO concentrations. The unexpected CO dependence of the rates in the second step supports a multistep mechanism, in which the 5-coordinate CO-heme is led by CO release from a putative bis-carbonyl intermediate that is likely provided by the binding of a second CO to the 6-coordinate CO-heme. This mechanism provides a new aspect on the activation of sGC by CO.

      DOI: 10.1021/acs.biochem.7b01240

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    • Essential Role of the ε Subunit for Reversible Chemo-Mechanical Coupling in F<sub>1</sub>-ATPase. 査読有り 国際誌

      Watanabe R, Genda M, Kato-Yamada Y, Noji H

      Biophysical journal114 ( 1 ) 178 - 187   2018年1月9日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.1016/j.bpj.2017.11.004

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    • The structural basis of a high affinity ATP binding ε subunit from a bacterial ATP synthase. 査読有り 国際誌

      Krah A, Kato-Yamada Y, Takada S

      PloS one12 ( 5 ) e0177907   2017年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.1371/journal.pone.0177907

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    • Pressure adaptation of 3-isopropylmalate dehydrogenase from an extremely piezophilic bacterium is attributed to a single amino acid substitution. 査読有り 国際誌

      Yuki Hamajima, Takayuki Nagae, Nobuhisa Watanabe, Eiji Ohmae, Yasuyuki Kato-Yamada, Chiaki Kato

      Extremophiles : life under extreme conditions20 ( 2 ) 177 - 86   2016年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER JAPAN KK  

      3-Isopropylmalate dehydrogenase (IPMDH) from the extreme piezophile Shewanella benthica (SbIPMDH) is more pressure-tolerant than that from the atmospheric pressure-adapted Shewanella oneidensis (SoIPMDH). To understand the molecular mechanisms of this pressure tolerance, we analyzed mutated enzymes. The results indicate that only a single mutation at position 266, corresponding to Ala (SbIPMDH) and Ser (SoIPMDH), essentially affects activity under higher-pressure conditions. Structural analyses of SoIPMDH suggests that penetration of three water molecules into the cleft around Ser266 under high-pressure conditions could reduce the activity of the wild-type enzyme; however, no water molecule is observed in the Ala266 mutant.

      DOI: 10.1007/s00792-016-0811-4

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    • Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis. 査読有り 国際誌

      Genki Akanuma, Yuka Kazo, Kazumi Tagami, Hirona Hiraoka, Koichi Yano, Shota Suzuki, Ryo Hanai, Hideaki Nanamiya, Yasuyuki Kato-Yamada, Fujio Kawamura

      Microbiology (Reading, England)162 ( 3 ) 448 - 458   2016年3月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:MICROBIOLOGY SOC  

      Ribosome dimers are a translationally inactive form of ribosomes found in Escherichia coli and many other bacterial cells. In this study, we found that the 70S ribosomes of Bacillus subtilis dimerized during the early stationary phase and these dimers remained in the cytoplasm until regrowth was initiated. Ribosome dimerization during the stationary phase required the hpf gene, which encodes a homologue of the E. coli hibernation-promoting factor (Hpf). The expression of hpf was induced at an early stationary phase and its expression was observed throughout the rest of the experimental period, including the entire 6 h of the stationary phase. Ribosome dimerization followed the induction of hpf in WT cells, but the dimerization was impaired in cells harbouring a deletion in the hpf gene. Although the absence of ribosome dimerization in these Hpf-deficient cells did not affect their viability in the stationary phase, their ability to regrow from the stationary phase decreased. Thus, following the transfer of stationary-phase cells to fresh LB medium, Δhpf mutant cells grew slower than WT cells. This observed lag in growth of Δhpf cells was probably due to a delay in restoring their translational activity. During regrowth, the abundance of ribosome dimers in WT cells decreased with a concomitant increase in the abundance of 70S ribosomes and growth rate. These results suggest that the ribosome dimers, by providing 70S ribosomes to the cells, play an important role in facilitating rapid and efficient regrowth of cells under nutrient-rich conditions.

      DOI: 10.1099/mic.0.000234

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    • High affinity nucleotide-binding mutant of the ε subunit of thermophilic F1-ATPase 査読有り 国際誌

      Yasuyuki Kato-Yamada

      Biochemical and Biophysical Research Communications469 ( 4 ) 1129 - 32   2016年1月22日

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      担当区分:筆頭著者, 最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier Inc.  

      Specific ATP binding to the ε subunit of thermophilic F1-ATPase has been utilized for the biosensors of
      ATP in vivo. I report here that the ε subunit containing R103A/R115A mutations can bind ATP with a
      dissociation constant at 52 nM, which is two orders of magnitude higher affinity than the wild type. The
      mutant retained specificity for ATP; ADP and GTP bound to the mutant with dissociation constants 16
      and 53 muM, respectively. Thus, the mutant would be a good platform for various types of nucleotide
      biosensor with appropriate modifications.

      DOI: 10.1016/j.bbrc.2015.12.121

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    • Pressure effects on the chimeric 3-isopropylmalate dehydrogenases of the deep-sea piezophilic Shewanella benthica and the atmospheric pressure-adapted Shewanella oneidensis. 査読有り 国際誌

      Yuki Hamajima, Takayuki Nagae, Nobuhisa Watanabe, Yasuyuki Kato-Yamada, Takeo Imai, Chiaki Kato

      Bioscience, biotechnology, and biochemistry78 ( 3 ) 469 - 71   2014年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:TAYLOR & FRANCIS LTD  

      The chimeric 3-isopropylmalate dehydrogenase enzymes were constructed from the deep-sea piezophilic Shewanella benthica and the shallow water Shewanella oneidensis genes. The properties of the enzymatic activities under pressure conditions indicated that the central region, which contained the active center and the dimer forming domains, was shown to be the most important region for pressure tolerance in the deep-sea enzyme.

      DOI: 10.1080/09168451.2014.890033

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    • Severe MgADP inhibition of Bacillus subtilis F1-ATPase is not due to the absence of nucleotide binding to the noncatalytic nucleotide binding sites. 査読有り 国際誌

      Toru Ishikawa, Yasuyuki Kato-Yamada

      PloS one9 ( 9 ) e107197   2014年

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:PUBLIC LIBRARY SCIENCE  

      F1-ATPase from Bacillus subtilis (BF1) is severely suppressed by the MgADP inhibition. Here, we have tested if this is due to the loss of nucleotide binding to the noncatalytic site that is required for the activation. Measurements with a tryptophan mutant of BF1 indicated that the noncatalytic sites could bind ATP normally. Furthermore, the mutant BF1 that cannot bind ATP to the noncatalytic sites showed much lower ATPase activity. It was concluded that the cause of strong MgADP inhibition of BF1 is not the weak nucleotide binding to the noncatalytic sites but the other steps required for the activation.

      DOI: 10.1371/journal.pone.0107197

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    • ε Subunit of Bacillus subtilis F1-ATPase relieves MgADP inhibition 査読有り 国際誌

      Junya Mizumoto, Yuka Kikuchi, Yo-Hei Nakanishi, Naoto Mouri, Anrong Cai, Tokushiro Ohta, Takamitsu Haruyama, Yasuyuki Kato-Yamada

      PLOS ONE8 ( 8 ) e73888   2013年

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Public Library of Science  

      DOI: 10.1371/journal.pone.0073888

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    • Hydrophobic shield on the molecular surface enhances thermal stability of ferredoxin of Cyanidioschyzon merolae 査読有り

      Yuko Ueno, Yasuyuki Kato-Yamada, Takeo Imai

      Journal of Japanese Society for Extremophiles11   59 - 63   2012年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • ATP binding to the ϵ subunit of thermophilic ATP synthase is crucial for efficient coupling of ATPase and H+ pump activities. 査読有り 国際誌

      Fumitaka Kadoya, Shigeyuki Kato, Kei Watanabe, Yasuyuki Kato-Yamada

      The Biochemical journal437 ( 1 ) 135 - 40   2011年7月1日

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:PORTLAND PRESS LTD  

      ATP binding to the ϵ subunit of F1-ATPase, a soluble subcomplex of TFoF1 (FoF1-ATPase synthase from the thermophilic Bacillus strain PS3), affects the regulation of F1-ATPase activity by stabilizing the compact, ATPase-active, form of the ϵ subunit [Kato, S., Yoshida, M. and Kato-Yamada, Y. (2007) J. Biol. Chem. 282, 37618-37623]. In the present study, we report how ATP binding to the ϵ subunit affects ATPase and H+ pumping activities in the holoenzyme TFoF1. Wild-type TFoF1 showed significant H+ pumping activity when ATP was used as the substrate. However, GTP, which bound poorly to the ϵ subunit, did not support efficient H+ pumping. Addition of small amounts of ATP to the GTP substrate restored coupling between GTPase and H+ pumping activities. Similar uncoupling was observed when TFoF1 contained an ATP-binding-deficient ϵ subunit, even with ATP as a substrate. Further analysis suggested that the compact conformation of the ϵ subunit induced by ATP binding was required to couple ATPase and H+ pumping activities in TFoF1 unless the ϵ subunit was in its extended-state conformation. The present study reveals a novel role of the ϵ subunit as an ATP-sensitive regulator of the coupling of ATPase and H+ pumping activities of TFoF1.

      DOI: 10.1042/BJ20110443

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    • Conformational transitions of subunit epsilon in ATP synthase from thermophilic Bacillus PS3. 査読有り 国際誌

      Boris A Feniouk, Yasuyuki Kato-Yamada, Masasuke Yoshida, Toshiharu Suzuki

      Biophysical journal98 ( 3 ) 434 - 42   2010年2月3日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:CELL PRESS  

      Subunit epsilon of bacterial and chloroplast F(O)F(1)-ATP synthase is responsible for inhibition of ATPase activity. In Bacillus PS3 enzyme, subunit epsilon can adopt two conformations. In the "extended", inhibitory conformation, its two C-terminal alpha-helices are stretched along subunit gamma. In the "contracted", noninhibitory conformation, these helices form a hairpin. The transition of subunit epsilon from an extended to a contracted state was studied in ATP synthase incorporated in Bacillus PS3 membranes at 59 degrees C. Fluorescence energy resonance transfer between fluorophores introduced in the C-terminus of subunit epsilon and in the N-terminus of subunit gamma was used to follow the conformational transition in real time. It was found that ATP induced the conformational transition from the extended to the contracted state (half-maximum transition extent at 140 microM ATP). ADP could neither prevent nor reverse the ATP-induced conformational change, but it did slow it down. Acid residues in the DELSEED region of subunit beta were found to stabilize the extended conformation of epsilon. Binding of ATP directly to epsilon was not essential for the ATP-induced conformational change. The ATP concentration necessary for the half-maximal transition (140 microM) suggests that subunit epsilon probably adopts the extended state and strongly inhibits ATP hydrolysis only when the intracellular ATP level drops significantly below the normal value.

      DOI: 10.1016/j.bpj.2009.10.023

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    • Inhibition of thermophilic F1-ATPase by the ε subunit takes different path from the ADP-Mg inhibition. 査読有り

      Takamitsu Haruyama, Yoko Hirono-Hara, Yasuyuki Kato-Yamada

      Biophysics (Nagoya-shi, Japan)6   59 - 65   2010年

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      The F1-ATPase, the soluble part of FoF1-ATP synthase, is a rotary molecular motor consisting of α3β3γδε. The γ and ε subunits rotate relative to the α3β3δ sub-complex on ATP hydrolysis by the β subunit. The ε subunit is known as an endogenous inhibitor of the ATPase activity of the F1-ATPase and is believed to function as a regulator of the ATP synthase. This inhibition by the ε subunit (ε inhibition) of F1-ATPase from thermophilic Bacillus PS3 was analyzed by single molecule measurements. By using a mutant ε subunit deficient in ATP binding, reversible transitions between active and inactive states were observed. Analysis of pause and rotation durations showed that the ε inhibition takes a different path from the ADP-Mg inhibition. Furthermore, the addition of the mutant ε subunit to the α3β3γ sub-complex was found to facilitate recovery of the ATPase activity from the ADP-Mg inhibition. Thus, it was concluded that these two inhibitions are essentially exclusive of each other.

      DOI: 10.2142/biophysics.6.59

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    • Modulation of nucleotide binding to the catalytic sites of thermophilic F(1)-ATPase by the epsilon subunit: implication for the role of the epsilon subunit in ATP synthesis. 査読有り 国際誌

      Taichi Yasuno, Eiro Muneyuki, Masasuke Yoshida, Yasuyuki Kato-Yamada

      Biochemical and biophysical research communications390 ( 2 ) 230 - 4   2009年12月11日

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ACADEMIC PRESS INC ELSEVIER SCIENCE  

      Effect of epsilon subunit on the nucleotide binding to the catalytic sites of F(1)-ATPase from the thermophilic Bacillus PS3 (TF(1)) has been tested by using alpha(3)beta(3)gamma and alpha(3)beta(3)gammaepsilon complexes of TF(1) containing betaTyr341 to Trp substitution. The nucleotide binding was assessed with fluorescence quenching of the introduced Trp. The presence of the epsilon subunit weakened ADP binding to each catalytic site, especially to the highest affinity site. This effect was also observed when GDP or IDP was used. The ratio of the affinity of the lowest to the highest nucleotide binding sites had changed two orders of magnitude by the epsilon subunit. The differences may relate to the energy required for the binding change in the ATP synthesis reaction and contribute to the efficient ATP synthesis.

      DOI: 10.1016/j.bbrc.2009.09.092

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    • Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators. 査読有り 国際誌

      Hiromi Imamura, Kim P Huynh Nhat, Hiroko Togawa, Kenta Saito, Ryota Iino, Yasuyuki Kato-Yamada, Takeharu Nagai, Hiroyuki Noji

      Proceedings of the National Academy of Sciences of the United States of America106 ( 37 ) 15651 - 6   2009年9月15日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATL ACAD SCIENCES  

      Adenosine 5'-triphosphate (ATP) is the major energy currency of cells and is involved in many cellular processes. However, there is no method for real-time monitoring of ATP levels inside individual living cells. To visualize ATP levels, we generated a series of fluorescence resonance energy transfer (FRET)-based indicators for ATP that were composed of the epsilon subunit of the bacterial F(o)F(1)-ATP synthase sandwiched by the cyan- and yellow-fluorescent proteins. The indicators, named ATeams, had apparent dissociation constants for ATP ranging from 7.4 muM to 3.3 mM. By targeting ATeams to different subcellular compartments, we unexpectedly found that ATP levels in the mitochondrial matrix of HeLa cells are significantly lower than those of cytoplasm and nucleus. We also succeeded in measuring changes in the ATP level inside single HeLa cells after treatment with inhibitors of glycolysis and/or oxidative phosphorylation, revealing that glycolysis is the major ATP-generating pathway of the cells grown in glucose-rich medium. This was also confirmed by an experiment using oligomycin A, an inhibitor of F(o)F(1)-ATP synthase. In addition, it was demonstrated that HeLa cells change ATP-generating pathway in response to changes of nutrition in the environment.

      DOI: 10.1073/pnas.0904764106

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    • Role of the ε Subunit of Thermophilic F1-ATPase as a Sensor for ATP. 査読有り 国際誌

      Kato S, Yoshida M, Kato-Yamada Y

      J. Biol. Chem.282 ( 52 ) 37618 - 23   2007年12月28日

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • Structures of the thermophilic F1-ATPase ε subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1. 査読有り 国際誌

      Yagi H, Kajiwara N, Tanaka H, Tsukihara T, Kato-Yamada Y, Yoshida M, Akutsu H

      Proc. Natl. Acad. Sci., U.S.A.104 ( 27 ) 11233 - 8   2007年7月3日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • γε sub-complex of thermophilic ATP synthase has the ability to bind ATP. 査読有り 国際誌

      Iizuka S, Kato S, Yoshida M, Kato-Yamada Y

      Biochem. Biophys. Res. Commun.349 ( 4 ) 1368 - 71   2006年11月3日

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      担当区分:最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.1016/j.bbrc.2006.09.001

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    • Isolated ε Subunit of Bacillus subtilis F1-ATPase Binds ATP. 査読有り 国際誌

      Kato-Yamada Y

      FEBS Lett.579 ( 30 ) 6875 - 8   2005年12月19日

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      担当区分:筆頭著者, 最終著者, 責任著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.1016/j.febslet.2005.11.036

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    • Real Time Monitoring of Conformational Dynamics of the ε Subunit in F1-ATPase. 査読有り 国際誌

      Iino R, Murakami T, Iizuka S, Kato-Yamada Y, Suzuki T, Yoshida M

      J. Biol. Chem.280 ( 48 ) 40130 - 4   2005年12月2日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      DOI: 10.1074/jbc.M506160200

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    • Highly coupled ATP synthesis by F1-ATPase single molecules. 査読有り 国際誌

      Yannick Rondelez, Guillaume Tresset, Takako Nakashima, Yasuyuki Kato-Yamada, Hiroyuki Fujita, Shoji Takeuchi, Hiroyuki Noji

      Nature433 ( 7027 ) 773 - 7   2005年2月17日

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:NATURE PUBLISHING GROUP  

      F1-ATPase is the smallest known rotary motor, and it rotates in an anticlockwise direction as it hydrolyses ATP. Single-molecule experiments point towards three catalytic events per turn, in agreement with the molecular structure of the complex. The physiological function of F1 is ATP synthesis. In the ubiquitous F0F1 complex, this energetically uphill reaction is driven by F0, the partner motor of F1, which forces the backward (clockwise) rotation of F1, leading to ATP synthesis. Here, we have devised an experiment combining single-molecule manipulation and microfabrication techniques to measure the yield of this mechanochemical transformation. Single F1 molecules were enclosed in femtolitre-sized hermetic chambers and rotated in a clockwise direction using magnetic tweezers. When the magnetic field was switched off, the F1 molecule underwent anticlockwise rotation at a speed proportional to the amount of synthesized ATP. At 10 Hz, the mechanochemical coupling efficiency was low for the alpha3beta3gamma subcomplex (F1-epsilon)), but reached up to 77% after reconstitution with the epsilon-subunit (F1+epsilon)). We provide here direct evidence that F1 is designed to tightly couple its catalytic reactions with the mechanical rotation. Our results suggest that the epsilon-subunit has an essential function during ATP synthesis.

      DOI: 10.1038/nature03277

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    • Ultra-small chamber for single-molecule detection of biological reaction

      Hiroyuki Noji, Yannick Rondelez, Takako Nakashima, Guillaume Tresset, Kazuhito Tabata, Yasuyuki Kato-Yamada, Hiroyuki Fujita, Shoji Takeuchi

      e-Journal of Surface Science and Nanotechnology3   79 - 81   2005年

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      掲載種別:研究論文(学術雑誌)   出版者・発行元:Surface Science Society Japan  

      DOI: 10.1380/ejssnt.2005.79

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    • Planar lipid bilayer reconstitution with a micro-fluidic system. 国際誌

      Hiroaki Suzuki, Kazuhito Tabata, Yasuyuki Kato-Yamada, Hiroyuki Noji, Shoji Takeuchi

      Lab on a chip4 ( 5 ) 502 - 5   2004年10月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

      A planar lipid bilayer which is widely used for the electrophysiological study of membrane proteins in laboratories is reconstituted using a micro-fluidic system, in a manner that is suitable for automated processing. We fabricated micro-channels on both sides of the substrate, which are connected through a 100-200 microm aperture, and showed that the bilayer can be formed at the aperture by flowing the lipid solution and buffer, alternately. Parylene coating is found to be suitable for both bilayer formation and electric noise reduction. Future applications include a high-sensitivity ion sensor chip and a high-throughput drug screening device.

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    • Planar lipid bilayer reconstitution with a micro-fluidic system 査読有り

      H Suzuki, K Tabata, Y Kato-Yamada, H Noji, S Takeuchi

      LAB ON A CHIP4 ( 5 ) 502 - 505   2004年

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      記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ROYAL SOC CHEMISTRY  

      A planar lipid bilayer which is widely used for the electrophysiological study of membrane proteins in laboratories is reconstituted using a micro-fluidic system, in a manner that is suitable for automated processing. We fabricated micro-channels on both sides of the substrate, which are connected through a 100-200 mm aperture, and showed that the bilayer can be formed at the aperture by flowing the lipid solution and buffer, alternately. Parylene coating is found to be suitable for both bilayer formation and electric noise reduction. Future applications include a high-sensitivity ion sensor chip and a high-throughput drug screening device.

      DOI: 10.1039/b405967k

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    • Isolated ε Subunit of Thermophilic F1 -ATPase Binds ATP. 査読有り 国際誌

      Kato-Yamada Y, Yoshida M

      J. Biol. Chem.278 ( 38 ) 36013 - 6   2003年9月19日

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      担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • The Role of the βDELSEED Motif of F1 -ATPase; Propagation of the Inhibitory Effect of the ε Subunit. 査読有り

      Hara KY, Kato-Yamada Y, Kikuchi Y, Hisabori T, Yoshida M

      J. Biol. Chem.276 ( 26 ) 23969 - 23973   2001年6月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • Movement of the Helical Domain of the ε Subunit Is Required for the Activation of Thermophilic F1 -ATPase 査読有り

      Kato-Yamada Y, Yoshida M, Hisabori T

      J. Biol. Chem.275 ( 46 ) 35746 - 35750   2000年11月

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      担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • ε Subunit,an Endogenous Inhibitor of Bacterial F1-ATPase, Also Inhibits FoF1-ATPase 査読有り

      Kato-Yamada Y, Bald D, Koike M, Motohashi K, Hisabori T, Yoshida M

      J. Biol. Chem.274 ( 48 ) 33991 - 33994   1999年11月

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      担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • Direct Observation of the Rotation of ε Subunit in F1-ATPase 査読有り

      Kato-Yamada Y, Noji H, Yasuda R, Kinosita K Jr, Yoshida M

      J. Biol. Chem.273 ( 31 ) 19375 - 19377   1998年7月

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      担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • Thermophilic F1 -ATPase Is Activated without Dissociation of an Endogenous Inhibitor, ε Subunit 査読有り

      Kato Y, Matsui T, Tanaka N, Muneyuki E, Hisabori T, Yoshida M

      J. Biol. Chem.272 ( 40 ) 24906 - 24912   1997年10月

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      担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • The Regulatory Functions of the γ and ε Subunits from Chloroplast CF1 Are Transferred to the Core Complex, α3 β3 , from Thermophilic Bacterial F1 査読有り

      Hisabori T, Kato Y, Motohashi K, Kroth-Pancic P, Strotmann H, Amano T

      Eur. J. Biochem.247 ( 3 ) 1158 - 1165   1997年8月

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      記述言語:英語   掲載種別:研究論文(学術雑誌)  

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    • ANALYSIS OF TIME-DEPENDENT CHANGE OF ESCHERICHIA-COLI F1-ATPASE ACTIVITY AND ITS RELATIONSHIP WITH APPARENT NEGATIVE COOPERATIVITY 査読有り

      Y KATO, T SASAYAMA, E MUNEYUKI, M YOSHIDA

      BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS1231 ( 3 ) 275 - 281   1995年10月

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      担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

      Except for the case of gradual activation of EF(1) (F-1-ATPase from Escherichia coli) caused by the dissociation of the epsilon subunit [Laget, P.P. and Smith, J.B. (1979) Arch. Biochem. Biophys. 197, 83-89], EF(1) has long been thought not to show a time-dependent change in activity [Senior, A.E. et al. (1992) Arch. Biochem. Biophys. 297, 340-344]. Here, we report the time-dependent inactivation and activation of EF(1), which are apparently similar to those of mitochondrial F-1-ATPases [Vasilyeva, E.A. et al, (1982) Biochem. J. 202, 15-23]. Analysis of these changes as a function of ATP concentrations in relation to negative cooperativity revealed that the initial inactivation phase was attributable to the decrease in the V-max associated with the low K-m (around 10 mu M), and the following activation, probably due to the dissociation of the epsilon subunit, corresponded to the increase in the V-max associated with the high K-m (in the order of 100 mu M). Thus, the time-dependent change in EF(1) activity is closely related to the apparent negative cooperativity (multiple K-m values) of ATP hydrolysis.

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    MISC

    • ATP合成酵素の活性調節におけるεサブユニットの役割 招待有り

      山田 康之

      生化学81 ( 11 )   2009年11月

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      担当区分:筆頭著者, 最終著者, 責任著者   記述言語:日本語   掲載種別:記事・総説・解説・論説等(その他)   出版者・発行元:日本生化学会  

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    所属学協会

    •  
      American Society for Biochemistry and Molecular Biology

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    •  
      日本生物物理学会

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    •  
      日本生化学会

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    共同研究・競争的資金等の研究

    • ATP合成酵素のATPモーターとプロトンモーターをつなぐ分子内クラッチ

      日本学術振興会  科学研究費助成事業 

      山田 康之

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      2015年4月 - 現在

      担当区分:研究代表者  資金種別:競争的資金

      ATP合成酵素に見られる、条件的脱共役状態の分子機構を明らかにする。

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    • 枯草菌ATP合成酵素の活性調節の包括的理解

      日本学術振興会  科学研究費助成事業 

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      2011年4月 - 2016年3月

      資金種別:競争的資金

      枯草菌ATP合成酵素の活性調節機構の解明

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    • ATP合成酵素の回転モータ制御の分子機構

      文部科学省  科学研究費助成事業 

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      2006年4月 - 2011年3月

      資金種別:競争的資金

      代表:久堀徹

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    • ATP合成酵素のεサブユニットへのATP結合と活性調節

      日本学術振興会  科学研究費助成事業 

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      2006年4月 - 2008年3月

      資金種別:競争的資金

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    産業財産権

    • Fluorescently labeled fusion protein for assaying adenosine triphosphate.

      Hiroyuki Noji, Hiromi Imamura, Ryota Iino, Yasuyuki Yamada

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      特許番号/登録番号:US Patent 08524447  発行日:2013年9月3日

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