Masasuke Yoshida

Summary

Affiliation: Tokyo Institute of Technology
Country: Japan

Publications

  1. ncbi ATP synthase--a marvellous rotary engine of the cell
    M Yoshida
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    Nat Rev Mol Cell Biol 2:669-77. 2001
  2. ncbi [Life of proteins]
    Masasuke Yoshida
    Tanpakushitsu Kakusan Koso 50:66-77. 2005
  3. ncbi [Birth and maturation of proteins]
    Masasuke Yoshida
    Tanpakushitsu Kakusan Koso 49:821-8. 2004
  4. ncbi GroEL locked in a closed conformation by an interdomain cross-link can bind ATP and polypeptide but cannot process further reaction steps
    N Murai
    Tokyo Institute of Technology, Research Laboratory of Resources Utilization, R 1, 4259 Nagatsuta, Yokohama 226, Japan
    J Biol Chem 271:28229-34. 1996
  5. ncbi Leu309 plays a critical role in the encapsulation of substrate protein into the internal cavity of GroEL
    Ayumi Koike-Takeshita
    Chemical Resources Laboratory, Tokyo Institute of Technology, Midori ku, Yokohama, Japan
    J Biol Chem 281:962-7. 2006
  6. ncbi Determination of the number of active GroES subunits in the fused heptamer GroES required for interactions with GroEL
    Tatsuya Nojima
    Chemical Resources Laboratory R1 7, Tokyo Institute of Technology, Yokohama, Japan
    J Biol Chem 283:18385-92. 2008
  7. ncbi Kinetic mechanism of quinol oxidation by cytochrome bd studied with ubiquinone-2 analogs
    Yushi Matsumoto
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Midori ku, Yokohama 226 8503
    J Biochem 139:779-88. 2006
  8. ncbi ATP binding to nucleotide binding domain (NBD)1 of the ClpB chaperone induces motion of the long coiled-coil, stabilizes the hexamer, and activates NBD2
    Yo Hei Watanabe
    Chemical Resources Laboratory, R 1, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    J Biol Chem 280:24562-7. 2005
  9. ncbi ATP hydrolysis and synthesis of a rotary motor V-ATPase from Thermus thermophilus
    Masahiro Nakano
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori ku, Yokohama, Japan
    J Biol Chem 283:20789-96. 2008
  10. ncbi Catalysis and rotation of F1 motor: cleavage of ATP at the catalytic site occurs in 1 ms before 40 degree substep rotation
    Katsuya Shimabukuro
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
    Proc Natl Acad Sci U S A 100:14731-6. 2003

Collaborators

Detail Information

Publications97

  1. ncbi ATP synthase--a marvellous rotary engine of the cell
    M Yoshida
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    Nat Rev Mol Cell Biol 2:669-77. 2001
    ..The mechanisms by which rotation and catalysis are coupled in the working enzyme are now being unravelled on a molecular scale...
  2. ncbi [Life of proteins]
    Masasuke Yoshida
    Tanpakushitsu Kakusan Koso 50:66-77. 2005
  3. ncbi [Birth and maturation of proteins]
    Masasuke Yoshida
    Tanpakushitsu Kakusan Koso 49:821-8. 2004
  4. ncbi GroEL locked in a closed conformation by an interdomain cross-link can bind ATP and polypeptide but cannot process further reaction steps
    N Murai
    Tokyo Institute of Technology, Research Laboratory of Resources Utilization, R 1, 4259 Nagatsuta, Yokohama 226, Japan
    J Biol Chem 271:28229-34. 1996
    ....
  5. ncbi Leu309 plays a critical role in the encapsulation of substrate protein into the internal cavity of GroEL
    Ayumi Koike-Takeshita
    Chemical Resources Laboratory, Tokyo Institute of Technology, Midori ku, Yokohama, Japan
    J Biol Chem 281:962-7. 2006
    ..Thus, conformational communication between the two GroES contact sites, the H helix and the GXXLE region (through Leu(309)), appears to play a critical role in encapsulation of the substrate...
  6. ncbi Determination of the number of active GroES subunits in the fused heptamer GroES required for interactions with GroEL
    Tatsuya Nojima
    Chemical Resources Laboratory R1 7, Tokyo Institute of Technology, Yokohama, Japan
    J Biol Chem 283:18385-92. 2008
    ..These results indicate the presence of an intermediate GroEL/substrate/GroES complex in which the substrate and GroES bind to GroEL by sharing seven common binding sites...
  7. ncbi Kinetic mechanism of quinol oxidation by cytochrome bd studied with ubiquinone-2 analogs
    Yushi Matsumoto
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Midori ku, Yokohama 226 8503
    J Biochem 139:779-88. 2006
    ..These results indicate that the mechanism for the substrate oxidation by cytochrome bd is different from that of the heme-copper terminal quinol oxidase and is tightly coupled to dioxygen reduction chemistry...
  8. ncbi ATP binding to nucleotide binding domain (NBD)1 of the ClpB chaperone induces motion of the long coiled-coil, stabilizes the hexamer, and activates NBD2
    Yo Hei Watanabe
    Chemical Resources Laboratory, R 1, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    J Biol Chem 280:24562-7. 2005
    ..This motion results in stabilization of the hexamer form of ClpB and promotion of ATP hydrolysis at NBD2...
  9. ncbi ATP hydrolysis and synthesis of a rotary motor V-ATPase from Thermus thermophilus
    Masahiro Nakano
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori ku, Yokohama, Japan
    J Biol Chem 283:20789-96. 2008
    ..4 x 10(7) m(-1) s(-1)). The slower k(on)(ATP) than k(on)(ADP) and strong Mg-ADP inhibition may contribute to prevent wasteful consumption of ATP under in vivo conditions when the proton motive force collapses...
  10. ncbi Catalysis and rotation of F1 motor: cleavage of ATP at the catalytic site occurs in 1 ms before 40 degree substep rotation
    Katsuya Shimabukuro
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
    Proc Natl Acad Sci U S A 100:14731-6. 2003
    ..Thus, cleavage of ATP on F1 occurs in 1 ms during the interim dwell, and we call this interim dwell catalytic dwell...
  11. ncbi Structure of the whole cytosolic region of ATP-dependent protease FtsH
    Ryoji Suno
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226 8503, Japan
    Mol Cell 22:575-85. 2006
    ..The protease catalytic sites are accessible only through a tunnel following from the AAA+ domain of the adjacent subunit, raising a possibility of translocation of polypeptide substrate to the protease sites through this tunnel...
  12. ncbi Essential arginine residue of the F(o)-a subunit in F(o)F(1)-ATP synthase has a role to prevent the proton shortcut without c-ring rotation in the F(o) proton channel
    Noriyo Mitome
    Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
    Biochem J 430:171-7. 2010
    ..Thus the conserved arginine residue in F(o)-a ensures proton-coupled c-ring rotation by preventing a futile proton shortcut...
  13. ncbi ATP-driven stepwise rotation of FoF1-ATP synthase
    Hiroshi Ueno
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8503, Japan
    Proc Natl Acad Sci U S A 102:1333-8. 2005
    ..However, dwells at clearly defined angular positions were not observed under these conditions, indicating that inhibition by tributyltin chloride is complex...
  14. ncbi Probing open conformation of GroEL rings by cross-linking reveals single and double open ring structures of GroEL in ADP and ATP
    Tatsuya Nojima
    Chemical Resources Laboratory R1 7, Tokyo Institute of Technology, 4259 Nagatsuta, Midori ku, Yokohama 226 8503, Japan
    J Biol Chem 284:22834-9. 2009
    ..Substrate protein was unable to form a stable complex with GroEL(OO) and did not stimulate ATPase activity of GroEL. These results favor a model of the GroEL reaction cycle that includes a football complex as a critical intermediate...
  15. ncbi Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli
    Yushi Matsumoto
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Midori ku, Yokohama 226 8503, Japan
    J Biol Chem 281:1905-12. 2006
    ....
  16. ncbi Escherichia coli phage-shock protein A (PspA) binds to membrane phospholipids and repairs proton leakage of the damaged membranes
    Ryuji Kobayashi
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    Mol Microbiol 66:100-9. 2007
    ..All these effects were not observed for monomer PspA that was prepared by refolding of urea-denatured PspA. These results indicate that oligomers of PspA bind to membrane phospholipids and suppress proton leakage...
  17. ncbi Hsp104 binds to yeast Sup35 prion fiber but needs other factor(s) to sever it
    Yuji Inoue
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatuta, Yokohama 226 8503, Japan
    J Biol Chem 279:52319-23. 2004
    ..The reason of discrepancy from the above report is unknown but is possibly caused by different conformational subspecies of prion fibers...
  18. ncbi Trigonal DnaK-DnaJ complex versus free DnaK and DnaJ: heat stress converts the former to the latter, and only the latter can do disaggregation in cooperation with ClpB
    Yo Hei Watanabe
    Chemical Resources Laboratory, R 1, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    J Biol Chem 279:15723-7. 2004
    ..Thus, TClpB-assisted disaggregation activity belongs only to K+J, and TDafA is a potential thermosensor for converting the K.J complex to K+J in response to heat stress...
  19. ncbi Torque generation and utilization in motor enzyme F0F1-ATP synthase: half-torque F1 with short-sized pushrod helix and reduced ATP Synthesis by half-torque F0F1
    Eiji Usukura
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503
    J Biol Chem 287:1884-91. 2012
    ..The rate of synthesis varies widely among the three F(0)F(1)(1/2)s, which suggests that the rate reflects subtle conformational variations of individual mutants...
  20. ncbi Significance of the epsilon subunit in the thiol modulation of chloroplast ATP synthase
    Hiroki Konno
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503, Japan
    Biochem Biophys Res Commun 318:17-24. 2004
    ..In addition, a structural requirement for the redox regulation of ATP hydrolysis activity might be different from that for the ATP synthesis activity...
  21. ncbi Discrimination of ATP, ADP, and AMPPNP by chaperonin GroEL: hexokinase treatment revealed the exclusive role of ATP
    Fumihiro Motojima
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori ku, Yokohama 226 8503, Japan
    J Biol Chem 278:26648-54. 2003
    ..In the absence of hexokinase, apparent cis folding of rhodanese and malate dehydrogenase was observed in ADP and AMPPNP. Thus, the exclusive role of ATP in generation of the cis ternary complex is now evident...
  22. ncbi Stepping rotation of F(1)-ATPase with one, two, or three altered catalytic sites that bind ATP only slowly
    Takayuki Ariga
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8503, Japan
    J Biol Chem 277:24870-4. 2002
    ....
  23. ncbi Mechanism of inhibition of the V-type molecular motor by tributyltin chloride
    Mizuho Takeda
    Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan
    Biophys J 96:1210-7. 2009
    ..This is the first report to demonstrate that an inhibitor arrests an elementary step for rotary catalysis of a V-type ATP-driven rotary motor...
  24. ncbi Thermophilic ATP synthase has a decamer c-ring: indication of noninteger 10:3 H+/ATP ratio and permissive elastic coupling
    Noriyo Mitome
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8503, Japan
    Proc Natl Acad Sci U S A 101:12159-64. 2004
    ..This step-mismatch necessitates elastic twisting of the rotor shaft (and/or the side stalk) during rotation and permissive coupling between unit rotations by H(+) transport at F(o) and elementary events in catalysis at F(1)...
  25. ncbi Origin of apparent negative cooperativity of F(1)-ATPase
    Sakurako Ono
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, 226-8503 Yokohama, Japan
    Biochim Biophys Acta 1607:35-44. 2003
    ..Thus, the frequently observed K(m)'s of 100-300 microM and 1-30 microM range for wild-type F(1)-ATPase correspond to ATP binding to a noncatalytic site and catalytic site, respectively...
  26. ncbi In vitro assay for fragmentation of amyloid fibers of yeast prion protein
    Yuji Inoue
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsutacho, Yokohama 226-8503, Japan
    Methods 39:56-60. 2006
    ..Fragmentation of the fibers results in release of fiber fragments into the medium, which are then quantified by immunoblotting. This method is versatile for other amyloid fibers...
  27. ncbi ATP synthase that lacks F0a-subunit: isolation, properties, and indication of F0b2-subunits as an anchor rail of a rotating c-ring
    Sakurako Ono
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8503, Japan
    J Biol Chem 279:33409-12. 2004
    ..Functional F1F0 is easily reconstituted from purified F0a and F1F0(-a), and thus F0a can bind to its proper location on F1F0(-a) without a large rearrangement of other-subunits...
  28. ncbi Effect of epsilon subunit on the rotation of thermophilic Bacillus F1-ATPase
    Masato Tsumuraya
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    FEBS Lett 583:1121-6. 2009
    ..It appears that epsilon undergoes reversible transition to the inhibitory form at [ATP] below K(d)...
  29. ncbi BeF(x) stops the chaperonin cycle of GroEL-GroES and generates a complex with double folding chambers
    Hideki Taguchi
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8503, Japan
    J Biol Chem 279:45737-43. 2004
    ..Thus, BeF(x) stabilizes two GroEL-GroES complexes; one with a single folding chamber and the other with double folding chambers. These results shed light on the intermediate ADP.P(i) nucleotide states in the functional cycle of GroEL...
  30. ncbi Isolated epsilon subunit of thermophilic F1-ATPase binds ATP
    Yasuyuki Kato-Yamada
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
    J Biol Chem 278:36013-6. 2003
    ..Although ATP binding to the isolated epsilon subunits from other organisms has not been detected under the same conditions, a possibility emerges that the epsilon subunit acts as a built in cellular ATP level sensor of F0F1-ATP synthase...
  31. ncbi UncI protein can mediate ring-assembly of c-subunits of FoF1-ATP synthase in vitro
    Yoko Ozaki
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori ku, Yokohama 226 8503, Japan
    Biochem Biophys Res Commun 367:663-6. 2008
    ..Fusion of the two kinds of liposomes, one containing only unassembled c-subunit and the other only UncI, resulted in gradual formation of c-ring. Thus, UncI alone can mediate in vitro post-translational c-ring assembly...
  32. ncbi Ribosomal protein L2 associates with E. coli HtpG and activates its ATPase activity
    Yuko Motojima-Miyazaki
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori ku, Yokohama 226 8503, Japan
    Biochem Biophys Res Commun 400:241-5. 2010
    ..The ATPase of HtpG at increasing concentration of L2 indicated that an L2 molecule bound to a dimer HtpG with apparent K(D) of 0.3 μM at 100mM KCl and 3.3 μM at 200 mM KCl...
  33. ncbi F1-ATPase changes its conformations upon phosphate release
    Tomoko Masaike
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8503, Japan
    J Biol Chem 277:21643-9. 2002
    ..This is the first evidence that the beta subunit changes its conformation upon phosphate release, which may share a common mechanism of exerting motility with other motor proteins...
  34. ncbi Trigger factor from Thermus thermophilus is a Zn2+-dependent chaperone
    Ryoji Suno
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226 8503, Japan
    J Biol Chem 279:6380-4. 2004
    ..5 mol Zn2+/mol TF. The folding-arrest activity of TF that was saturated with Zn2+ (approximately 1 mol/mol TF) was twice as efficient as that of untreated TF. Thus, chaperone activity of thermophilic TF is Zn2+-dependent...
  35. ncbi Stabilization of FtsH-unfolded protein complex by binding of ATP and blocking of protease
    Hisayoshi Makyio
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, 226-8503, Yokohama, Japan
    Biochem Biophys Res Commun 296:8-12. 2002
    ..The FtsH without mutation at Glu-419 did not produce a stable complex with casein in the presence of any nucleotides tested and therefore it appears that blocking proteolysis also contributes to stabilization of the complex...
  36. ncbi F1-ATPase rotates by an asymmetric, sequential mechanism using all three catalytic subunits
    Takayuki Ariga
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226 8503, Japan
    Nat Struct Mol Biol 14:841-6. 2007
    ....
  37. ncbi Dodecamer rotor ring defines H+/ATP ratio for ATP synthesis of prokaryotic V-ATPase from Thermus thermophilus
    Masashi Toei
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori ku, Yokohama 226 8503, Japan
    Proc Natl Acad Sci U S A 104:20256-61. 2007
    ..0-A resolution showed the presence of 12 V(o)-c subunits, each composed of two transmembrane helices. These results indicate that symmetry mismatch between the rotor and catalytic domains is not obligatory for rotary ATPases/synthases...
  38. ncbi Effect of external torque on the ATP-driven rotation of F1-ATPase
    Takahiro Watanabe-Nakayama
    Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama 226 8503, Japan
    Biochem Biophys Res Commun 366:951-7. 2008
    ..Due to the temperature rise during experiment, quantitative interpretation of the data is difficult, but we found that the apparent rate constant of ATP binding clearly decreased by hindering torque and increased by assisting torque...
  39. ncbi F(0) of ATP synthase is a rotary proton channel. Obligatory coupling of proton translocation with rotation of c-subunit ring
    Toshiharu Suzuki
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226-8503, Japan
    J Biol Chem 277:13281-5. 2002
    ..Thus, rotation of the c-oligomer ring relative to subunit b is obligatory for proton translocation; if there is no rotation of the c-ring there is no proton flow through F(0)...
  40. ncbi The presence of phosphate at a catalytic site suppresses the formation of the MgADP-inhibited form of F(1)-ATPase
    Noriyo Mitome
    Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan
    Eur J Biochem 269:53-60. 2002
    ..It is likely that the presence of P(i) at a catalytic site shifts the equilibrium from the MgADP-inhibited form to the enzyme-MgADP-P(i) complex, an active intermediate in the catalytic cycle...
  41. ncbi [Mechanism of prion-fibril formation]
    Yuji Inoue
    Tanpakushitsu Kakusan Koso 49:1108-9. 2004
  42. ncbi Rotation of the proteolipid ring in the V-ATPase
    Ken Yokoyama
    ATP System Project, Exploratory Research for Advanced Technology ERATO, Japan Science and Technology Corporation JST, 5800 3 Nagatsuta, Midori ku, Yokohama 226 0026, Japan
    J Biol Chem 278:24255-8. 2003
    ..0 rev/s in average at 4 mm ATP and was abolished by N',N'-dicyclohexylcarbodiimide treatment. Thus, the rotation of the central stalk in V1 accompanies rotation of a proteolipid ring of V0 in the functioning V0V1-ATPase...
  43. ncbi [Disaggregation of protein aggregates by ClpB chaperone]
    Yo-hei Watanabe
    Tanpakushitsu Kakusan Koso 49:1059-61. 2004
  44. ncbi Subunit arrangement in V-ATPase from Thermus thermophilus
    Ken Yokoyama
    ATP System Project, ERATO, Japan Science and Technology Corp, 5800 3 Nagatsuta, Midori ku, Yokohama 226 0026, Japan
    J Biol Chem 278:42686-91. 2003
    ..and Tamakoshi, M. (2003) J. Biol. Chem. 278, 24255-24258), we propose that C, D, F, and L subunits constitute the central rotor shaft and A, B, E, G, and I subunits comprise the surrounding stator apparatus in the V0V1-ATPase...
  45. ncbi The role of subunit epsilon in the catalysis and regulation of FOF1-ATP synthase
    Boris A Feniouk
    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation JST, 5800 3 Nagatsuta, Midori ku, Yokohama 226 0026, Japan
    Biochim Biophys Acta 1757:326-38. 2006
    ..Multiple functions of subunit epsilon, its role in the difference between the catalytic pathways of ATP synthesis and hydrolysis and its influence on the inhibition of ATP hydrolysis by ADP are also discussed...
  46. ncbi The gamma subunit in chloroplast F(1)-ATPase can rotate in a unidirectional and counter-clockwise manner
    T Hisabori
    Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Nagatsuta 4259, Midori ku, Yokohama, Japan
    FEBS Lett 463:35-8. 1999
    ..We conclude that the rotation of the gamma subunit in the F(1)-motor is a ubiquitous phenomenon in all F(1)-ATPases in prokaryotes as well as in eukaryotes...
  47. ncbi A new system for the measurement of electrogenicity produced by ion pumps using a thin polymer film: examination of wild type bacteriorhodopsin and the D96N mutant over a wide pH range
    E Muneyuki
    Research Laboratory of Resources Utilization, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
    FEBS Lett 427:109-14. 1998
    ..We also found that this film can be used as a substrate for atomic force microscopy (AFM) samples and hence the active purple membrane was observed with AFM...
  48. ncbi The heterogeneous interaction of substoichiometric TNP-ATP and F1-ATPase from Escherichia coli
    E Muneyuki
    Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama
    J Biochem 120:940-5. 1996
    ..Weaker affinity of the catalytic site for TNP-ATP may account for the heterogeneous binding and hydrolysis under the conditions described in this paper...
  49. ncbi Thiol modulation of the chloroplast ATP synthase is dependent on the energization of thylakoid membranes
    Hiroki Konno
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta, Midori ku, Yokohama, Japan
    Plant Cell Physiol 53:626-34. 2012
    ....
  50. ncbi beta-Helix is a likely core structure of yeast prion Sup35 amyloid fibers
    Aiko Kishimoto
    Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan
    Biochem Biophys Res Commun 315:739-45. 2004
    ..Thus, the core structure of these amyloid fibers made of the N domain is likely to be beta-helix nanotube as proposed by Perutz et al...
  51. ncbi Redox regulation of the rotation of F(1)-ATP synthase
    D Bald
    PRESTO, Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Japan
    J Biol Chem 276:39505-7. 2001
    ..These findings obtained by the single molecule analysis therefore provide new insights into the mechanisms of enzyme regulation...
  52. ncbi Molecular cloning, expression, and characterization of chaperonin-60 and chaperonin-10 from a thermophilic bacterium, Thermus thermophilus HB8
    K Amada
    Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama
    J Biochem 118:347-54. 1995
    ..th cpn60 was easily purified from T.th cpn60 oligomer by gel permeation chromatography. Thus-obtained T.th cpn60 monomer had an ATP-independent chaperone activity, as shown for T.th cpn60 monomer isolated from authentic holo-chaperonin...
  53. ncbi Roles of the two ATP binding sites of ClpB from Thermus thermophilus
    Yo Hei Watanabe
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226 8503, Japan
    J Biol Chem 277:5804-9. 2002
    ..4) Chaperone function of TClpB was lost when the WalkerA motif in each of the NBDs was mutated. Mutants in the WalkerB motifs of each NBD retained some chaperone activity...
  54. ncbi Single-molecule observation of protein-protein interactions in the chaperonin system
    H Taguchi
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
    Nat Biotechnol 19:861-5. 2001
    ..However, the release of GroES from GroEL occurred after a lag period ( approximately 3 s) that was not recognized in earlier bulk-phase studies. This observation suggests a new kinetic intermediate in the GroEL-GroES reaction pathway...
  55. ncbi Molecular cloning of phosphofructokinase 1 gene from a thermophilic bacterium, Thermus thermophilus
    J Xu
    Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan
    Biochem Biophys Res Commun 176:1313-8. 1991
    ..While almost all amino acid residues involved in substrate binding sites, which are assigned from crystal structures of other PFKs, are well conserved, some possibly important changes are found at subunit interfaces...
  56. ncbi Synchronized domain-opening motion of GroEL is essential for communication between the two rings
    K Shiseki
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, 226-8503, Japan
    J Biol Chem 276:11335-8. 2001
    ..Taken together, cooperative conformational transitions in GroEL rings ensure the functional communication between the two rings of GroEL...
  57. ncbi Molecular cloning of genes encoding major two subunits of a eubacterial V-type ATPase from Thermus thermophilus
    S Tsutsumi
    Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan
    Biochim Biophys Acta 1098:13-20. 1991
    ..The hypothesis that the differentiation of an ancestral ATPase into V-type and F0F1-ATPase occurred after the evolution of a primordial cell into archaebacteria and eubacteria should be modified accordingly...
  58. ncbi The membrane-associated ATPase from Sulfolobus acidocaldarius is distantly related to F1-ATPase as assessed from the primary structure of its alpha-subunit
    K Denda
    Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan
    J Biol Chem 263:6012-5. 1988
    ..Thus, the S. acidocaldarius ATPase and probably other archaebacterial ATPases also appear to belong to a new group of ion-translocating ATPases that has only a distant relationship to F1-ATPase...
  59. ncbi Pause and rotation of F(1)-ATPase during catalysis
    Y Hirono-Hara
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
    Proc Natl Acad Sci U S A 98:13649-54. 2001
    ..The pausing position of the gamma subunit deviates from the ATP-waiting position and is most likely the recently found intermediate 90 degrees position...
  60. ncbi The role of the betaDELSEED motif of F1-ATPase: propagation of the inhibitory effect of the epsilon subunit
    K Y Hara
    Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama, 226-8503, Japan
    J Biol Chem 276:23969-73. 2001
    ..We here conclude that the epsilon subunit exerts its inhibitory effect through the electrostatic interaction with the DELSEED motif of the beta subunit...
  61. ncbi Strong growth polarity of yeast prion fiber revealed by single fiber imaging
    Y Inoue
    Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226 8503, Japan
    J Biol Chem 276:35227-30. 2001
    ..These results indicate the polarity of Sup35 prion fibers and impose constraints on the models of fiber growth...
  62. ncbi Purification and molecular cloning of the group II chaperonin from the acidothermophilic archaeon, Sulfolobus sp. strain 7
    N Nakamura
    Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama, Japan
    Biochem Biophys Res Commun 236:727-32. 1997
    ..The chaperonin consists of two kinds of subunits, alpha and beta, the deduced amino acid sequences of which were highly homologous to those of TF56 and TF55 from Sulfolobus shibatae, respectively...
  63. ncbi A chaperonin from a thermophilic bacterium, Thermus thermophilus, that controls refoldings of several thermophilic enzymes
    H Taguchi
    Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Japan
    J Biol Chem 266:22411-8. 1991
    ..At temperatures below 20 degrees C, where spontaneous refoldings also occur, the chaperonin arrests the refolding but ATP does not induce refolding...
  64. ncbi Molecular cloning of the beta-subunit of a possible non-F0F1 type ATP synthase from the acidothermophilic archaebacterium, Sulfolobus acidocaldarius
    K Denda
    Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan
    J Biol Chem 263:17251-4. 1988
    ..acidocaldarius ATPase and F0F1-ATPases have been derived from a common ancestral ATPase...
  65. ncbi A novel factor required for the assembly of the DnaK and DnaJ chaperones of Thermus thermophilus
    K Motohashi
    Research Laboratory of Resources Utilization, R 1, Tokyo Institute of Technology, Nagatsuta 4259, Yokohama 226, Japan
    J Biol Chem 271:17343-8. 1996
    ..DafA. Even though a definite homolog of T.DafA has not been found in the data base, this finding raises a possibility that interaction between DnaK and DnaJ chaperones in other organisms is also mediated by a small protein yet unnoticed...
  66. ncbi Archaeal group II chaperonin mediates protein folding in the cis-cavity without a detachable GroES-like co-chaperonin
    Takao Yoshida
    Kamaishi Laboratories, Marine Biotechnology Institute Co. Ltd, 3-75-1 Heita, Kamaishi, 026-0001, Iwate, Japan
    J Mol Biol 315:73-85. 2002
    ..The present data indicate that, in the group II chaperonin of Thermococcus strain KS-1, the protein folding proceeds in its cis-ring in an ATP-dependent fashion without any co-chaperonin...
  67. ncbi Role of the epsilon subunit of thermophilic F1-ATPase as a sensor for ATP
    Shigeyuki Kato
    Department of Life Science, College of Science, Rikkyo St Paul s University, Tokyo, Japan
    J Biol Chem 282:37618-23. 2007
    ..These results clearly indicate that ATP binding to the epsilon subunit plays a regulatory role and that ATP binding may stabilize the ATPase-active form of TF(1) by fixing the epsilon subunit into the folded conformation...
  68. ncbi Temperature-sensitive reaction intermediate of F1-ATPase
    Rikiya Watanabe
    Department of Mechanical Engineering, University of Tokyo, Tokyo 113 8656, Japan
    EMBO Rep 9:84-90. 2008
    ..Conversely, the addition of inorganic phosphate caused a pause at an angle of +80 degrees from that of the intermediate state. These observations strongly suggest that the newly found reaction intermediate is an ADP-releasing step...
  69. ncbi The product of uncI gene in F1Fo-ATP synthase operon plays a chaperone-like role to assist c-ring assembly
    Toshiharu Suzuki
    ATP Synthesis Regulation Project, ICORP, Japan Science and Technology Corporation, Aomi 2 41, Tokyo 135 0064, Japan
    Proc Natl Acad Sci U S A 104:20776-81. 2007
    ..Na(+) induced dissociation of His-tagged UncI protein from c(11)-ring but not from c-monomers. These results show that UncI is a chaperone-like protein that assists c(11)-ring assembly from c-monomers in the membrane...
  70. ncbi Crystallization and preliminary X-ray crystallographic analysis of the Hsp100 chaperone ClpB from Thermus thermophilus
    Sukyeong Lee
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
    Acta Crystallogr D Biol Crystallogr 59:2334-6. 2003
    ..Complete native data sets have been collected from frozen crystals, which belonged to the primitive orthorhombic space group P2(1)2(1)2(1) with unit-cell parameters a = 109.2, b = 139.6, c = 213.0 A, alpha = beta = gamma = 90 degrees...
  71. ncbi Axle-less F1-ATPase rotates in the correct direction
    Shou Furuike
    Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku ku, Tokyo 169 8555, Japan
    Science 319:955-8. 2008
    ..Neither a fixed pivot nor a rigid axle was needed for rotation of F1-ATPase...
  72. ncbi Reconstitution in vitro of V1 complex of Thermus thermophilus V-ATPase revealed that ATP binding to the A subunit is crucial for V1 formation
    Hiromi Imamura
    ATP System Project, Exploratory Research for Advanced Technology (ERATO, Japan Science and Technology Agency (JST, 5800-3 Nagatsuta, Midori-ku, Yokohama 226-0026, Japan
    J Biol Chem 281:38582-91. 2006
    ..Kinetics of binding of a fluorescent ADP analog, N-methylanthraniloyl ADP (mant-ADP), to the monomeric A subunit also supported the rapid nucleotide binding to the A subunit...
  73. ncbi Revisiting the GroEL-GroES reaction cycle via the symmetric intermediate implied by novel aspects of the GroEL(D398A) mutant
    Ayumi Koike-Takeshita
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
    J Biol Chem 283:23774-81. 2008
    ..In light of these results, the current model of the GroEL-GroES reaction cycle via the asymmetric 1:1 GroEL-GroES complex deserves reexamination...
  74. ncbi Temperature dependence of the rotation and hydrolysis activities of F1-ATPase
    Shou Furuike
    Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku ku, Tokyo, Japan
    Biophys J 95:761-70. 2008
    ..Rapid inactivation at high temperatures is consistent with the physiological role of this enzyme, ATP synthesis, in the thermophile...
  75. ncbi Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation
    Kengo Adachi
    Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku ku, Tokyo 169 8555, Japan
    Cell 130:309-21. 2007
    ..This and other results suggest that the affinity for ADP also decreases with rotation, and thus ADP release contributes part of energy for rotation. Together with previous results, the coupling scheme is now basically complete...
  76. ncbi Structures of the thermophilic F1-ATPase epsilon subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1
    Hiromasa Yagi
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita 565 0871, Japan
    Proc Natl Acad Sci U S A 104:11233-8. 2007
    ..These results suggest that the epsilon C-terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of F(o)F(1)-ATP synthase...
  77. ncbi Single molecule energetics of F1-ATPase motor
    Eiro Muneyuki
    Department of Physics, Faculty of Science and Technology, Chuo University, Tokyo, Japan
    Biophys J 92:1806-12. 2007
    ..The results imply that microscopically defined work at a single molecule level cannot be directly compared with macroscopically defined free energy input...
  78. ncbi Rotation scheme of V1-motor is different from that of F1-motor
    Hiromi Imamura
    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Midori-ku, Yokohama
    Proc Natl Acad Sci U S A 102:17929-33. 2005
    ..Thus, the mechanochemical cycle of V(1) has marked differences to that of F(1)...
  79. ncbi Mechanically driven ATP synthesis by F1-ATPase
    Hiroyasu Itoh
    Tsukuba Research Laboratory, Hamamatsu Photonics KK, Joko, Hamamatsu 431 3103, Japan
    Nature 427:465-8. 2004
    ..This shows that a vectorial force (torque) working at one particular point on a protein machine can influence a chemical reaction occurring in physically remote catalytic sites, driving the reaction far from equilibrium...
  80. ncbi Structure of a central stalk subunit F of prokaryotic V-type ATPase/synthase from Thermus thermophilus
    Hisayoshi Makyio
    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yokohama, Japan
    EMBO J 24:3974-83. 2005
    ..Our results postulated that the subunit F is a regulatory subunit in the V-ATPase...
  81. ncbi An alternative reaction pathway of F1-ATPase suggested by rotation without 80 degrees/40 degrees substeps of a sluggish mutant at low ATP
    Katsuya Shimabukuro
    ATP System Project, Exploratory Research for Advanced Technology (ERATO, Japan Science and Technology Agency (JST, Yokohama 226-0026, Japan
    Biophys J 90:1028-32. 2006
    ..Thus, F(1)-ATPase can operate through (at least) two competing reaction pathways, not necessarily through a simple consecutive reaction...
  82. ncbi The F subunit of Thermus thermophilus V1-ATPase promotes ATPase activity but is not necessary for rotation
    Hiromi Imamura
    ATP System Project, Exploration Research for Advanced Technology, Japan Science and Technology Agency, 5800-3 Nagatsuta, Midori-ku, Yokohama 226-0026, Japan
    J Biol Chem 279:18085-90. 2004
    ..Thus, the F subunit binds peripherally to the D subunit, but promotes V(1)-ATPase catalysis...
  83. ncbi Real-time monitoring of conformational dynamics of the epsilon subunit in F1-ATPase
    Ryota Iino
    ATP System Project, ERATO, Japan Science and Technology Agency, Nagatsuta 5800-3, Yokohama 226-0026, Japan
    J Biol Chem 280:40130-4. 2005
    ..67 mm, a consistent value to assume that the epsilon subunit acts as a sensor of ATP concentration in the cell...
  84. ncbi GroEL mediates protein folding with a two successive timer mechanism
    Taro Ueno
    Department of Physics, School of Science and Engineering, Waseda University, 3 4 1 Okubo, Tokyo 169 8555, Japan
    Mol Cell 14:423-34. 2004
    ..ADP, GroES, and substrate depart GroEL after the second timer is complete. This mechanism explains how GroES binding to a GroEL-substrate complex encapsulates the substrate rather than allowing it to escape into solution...
  85. ncbi Conformational change of H+-ATPase beta monomer revealed on segmental isotope labeling NMR spectroscopy
    Hiromasa Yagi
    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
    J Am Chem Soc 126:16632-8. 2004
    ..The intrinsic conformational change of the beta subunit monomer induced by nucleotide binding must be one of the essential driving forces for the rotation of F1-ATPase...
  86. ncbi Probing conformations of the beta subunit of F0F1-ATP synthase in catalysis
    Tomoko Masaike
    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation (JST, 5800-3 Nagatsuta, Yokohama 226-0026, Japan
    Biochem Biophys Res Commun 342:800-7. 2006
    ....
  87. ncbi Chemomechanical coupling in F1-ATPase revealed by simultaneous observation of nucleotide kinetics and rotation
    Takayuki Nishizaka
    Kansai Advanced Research Center, Protein Biophysics Group, Iwaoka 588 2, Nishi ku, Kobe 651 2492, Japan
    Nat Struct Mol Biol 11:142-8. 2004
    ....
  88. ncbi Chemomechanical coupling in single-molecule F-type ATP synthase
    Ryota Iino
    The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
    J Bioenerg Biomembr 37:451-4. 2005
    ..It is plausible that the conformational change of epsilon switches the catalytic mode of F(0)F(1) for highly coupled ATP synthesis...
  89. ncbi Regulatory interplay between proton motive force, ADP, phosphate, and subunit epsilon in bacterial ATP synthase
    Boris A Feniouk
    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, Midori ku, Yokohama 226 0026, Japan
    J Biol Chem 282:764-72. 2007
    ..It appears that these features allow the enzyme to promptly respond to changes in the ATP:ADP ratio and in pmf levels in order to avoid potentially wasteful ATP hydrolysis in vivo...
  90. ncbi Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8
    Hajime Niwa
    Department of Structural Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka, Japan
    Structure 10:1415-23. 2002
    ....
  91. ncbi gammaepsilon Sub-complex of thermophilic ATP synthase has the ability to bind ATP
    Satoshi Iizuka
    Department of Life Science, College of Science, Rikkyo University, 3-34-1, Nishi-Ikebukuro, Tokyo 171-8501, Japan
    Biochem Biophys Res Commun 349:1368-71. 2006
    ..The results clearly showed that the gammaepsilon sub-complex can bind ATP...
  92. ncbi Dynamics of yeast prion aggregates in single living cells
    Shigeko Kawai-Noma
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, FSB401, 5 1 5 Kashiwanoha, Kashiwa, Chiba, 277 8562, Japan
    Genes Cells 11:1085-96. 2006
    ..Single-cell observations of the oligomer-based transmission provide a link between previous in vivo and in vitro analyses of the prion and shed light on the relationship between the protein conformation and the phenotype...
  93. ncbi Evidence for rotation of V1-ATPase
    Hiromi Imamura
    ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, 5800-3 Nagatsuta, Midori-ku, Yokohama 226-0026, Japan
    Proc Natl Acad Sci U S A 100:2312-5. 2003
    ..This study provides experimental evidence that V(o)V(1)-ATPase is a rotary motor and that both D and F subunits constitute a rotor shaft...
  94. ncbi F0F1-ATPase/synthase is geared to the synthesis mode by conformational rearrangement of epsilon subunit in response to proton motive force and ADP/ATP balance
    Toshiharu Suzuki
    ATP System Project, Exploratory Research for Advanced Technology (ERATO, Japan Science and Technology Corporation (JST, Nagatsuta 5800-2, Yokohama 226-0026, Japan
    J Biol Chem 278:46840-6. 2003
    ..Thus, responding to the increase of proton motive force and ADP, F0F1-ATPase/synthase would transform the epsilon subunit into the up-state conformation and change gear to the mode for ATP synthesis...
  95. ncbi The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state
    Sukyeong Lee
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 115:229-40. 2003
    ..Taken together, we propose a mechanism by which an ATP-driven conformational change is coupled to a large coiled-coil motion, which is indispensable for protein disaggregation...
  96. ncbi The rotor tip inside a bearing of a thermophilic F1-ATPase is dispensable for torque generation
    Mohammad Delawar Hossain
    Department of Physics, Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
    Biophys J 90:4195-203. 2006
    ..For torque generation, though not for rapid catalysis, most of the rotor-stator contacts on the deeper half of the penetrating portion of the gamma-subunit are dispensable...
  97. ncbi One rotary mechanism for F1-ATPase over ATP concentrations from millimolar down to nanomolar
    Naoyoshi Sakaki
    Department of Functional Molecular Science, The Graduate University for Advanced Studies, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
    Biophys J 88:2047-56. 2005
    ..Below 1 nM ATP, we observed less regular rotations, indicative of the appearance of another reaction scheme...