32 results on '"Masahiko Okuda"'
Search Results
2. Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones
- Author
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Masahiko Okuda, Yasuo Tsunaka, and Yoshifumi Nishimura
- Subjects
Structural Biology ,Biophysics ,Molecular Biology - Published
- 2022
3. Three human RNA polymerases interact with TFIIH via a common RPB6 subunit
- Author
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Hidefumi Suzuki, Yoshifumi Nishimura, Masahiko Okuda, Yuki Yamaguchi, and Tetsufumi Suwa
- Subjects
AcademicSubjects/SCI00010 ,Protein subunit ,NAR Breakthrough Article ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Genetics ,Humans ,Gene ,030304 developmental biology ,0303 health sciences ,Messenger RNA ,Binding Sites ,RNA ,Pleckstrin Homology Domains ,Cell biology ,Molecular Docking Simulation ,Transfer RNA ,Transcription factor II H ,RNA Polymerase II ,Transcription Factor TFIIH ,030217 neurology & neurosurgery ,Nucleotide excision repair ,HeLa Cells ,Protein Binding - Abstract
In eukaryotes, three RNA polymerases (RNAPs) play essential roles in the synthesis of various types of RNA: namely, RNAPI for rRNA; RNAPII for mRNA and most snRNAs; and RNAPIII for tRNA and other small RNAs. All three RNAPs possess a short flexible tail derived from their common subunit RPB6. However, the function of this shared N-terminal tail (NTT) is not clear. Here we show that NTT interacts with the PH domain (PH-D) of the p62 subunit of the general transcription/repair factor TFIIH, and present the structures of RPB6 unbound and bound to PH-D by nuclear magnetic resonance (NMR). Using available cryo-EM structures, we modelled the activated elongation complex of RNAPII bound to TFIIH. We also provide evidence that the recruitment of TFIIH to transcription sites through the p62–RPB6 interaction is a common mechanism for transcription-coupled nucleotide excision repair (TC-NER) of RNAPI- and RNAPII-transcribed genes. Moreover, point mutations in the RPB6 NTT cause a significant reduction in transcription of RNAPI-, RNAPII- and RNAPIII-transcribed genes. These and other results show that the p62–RPB6 interaction plays multiple roles in transcription, TC-NER, and cell proliferation, suggesting that TFIIH is engaged in all RNAP systems.
- Published
- 2022
4. Structural polymorphism of the PH domain in TFIIH.
- Author
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Masahiko Okuda and Yoshifumi Nishimura
- Abstract
The general transcription factor TFIIH is a multi-subunit complex involved in transcription, DNA repair, and cell cycle in eukaryotes. In the human p62 subunit and the budding yeast Saccharomyces cerevisiae Tfb1 subunit of TFIIH, the pleckstrin homology (PH) domain (hPH/scPH) recruits TFIIH to transcription-start and DNA-damage sites by interacting with an acidic intrinsically disordered region in transcription and repair factors. Whereas metazoan PH domains are highly conserved and adopt a similar structure, fungal PH domains are divergent and only the scPH structure is available. Here, we have determined the structure of the PH domain from Tfb1 of fission yeast Schizosaccharomyces pombe (spPH) by NMR. spPH holds an architecture, including the core and external backbone structures, that is closer to hPH than to scPH despite having higher amino acid sequence identity to scPH. In addition, the predicted target-binding site of spPH shares more amino acid similarity with scPH, but spPH contains several key residues identified in hPH as required for specific binding. Using chemical shift perturbation, we have identified binding modes of spPH to spTfa1, a homologue of hTFIIEa, and to spRhp41, a homologue of the repair factors hXPC and scRad4. Both spTfa1 and spRhp41 bind to a similar but distinct surface of spPH by modes that differ from those of target proteins binding to hPH and scPH, revealing that the PH domain of TFIIH interacts with its target proteins in a polymorphic manner in Metazoa, and budding and fission yeasts. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. Structural and dynamical insights into the PH domain of p62 in human TFIIH
- Author
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Masahiko Okuda, Mitsunori Ikeguchi, Jun-ichi Kurita, Toru Ekimoto, and Yoshifumi Nishimura
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0303 health sciences ,010304 chemical physics ,DNA repair ,AcademicSubjects/SCI00010 ,Protein subunit ,Protein domain ,Cryoelectron Microscopy ,Pleckstrin Homology Domains ,Biology ,Molecular Dynamics Simulation ,01 natural sciences ,Pleckstrin homology domain ,03 medical and health sciences ,Protein Domains ,Transcription (biology) ,Structural Biology ,0103 physical sciences ,Genetics ,Biophysics ,Transcription factor II H ,Humans ,Transcription factor ,Transcription Factor TFIIH ,030304 developmental biology ,Nucleotide excision repair - Abstract
TFIIH is a crucial transcription and DNA repair factor consisting of the seven-subunit core. The core subunit p62 contains a pleckstrin homology domain (PH-D), which is essential for locating TFIIH at transcription initiation and DNA damage sites, and two BSD (BTF2-like transcription factors, synapse-associated proteins and DOS2-like proteins) domains. A recent cryo-electron microscopy (cryo-EM) structure of human TFIIH visualized most parts of core, except for the PH-D. Here, by nuclear magnetic resonance spectroscopy we have established the solution structure of human p62 PH-D connected to the BSD1 domain by a highly flexible linker, suggesting the flexibility of PH-D in TFIIH. Based on this dynamic character, the PH-D was modeled in the cryo-EM structure to obtain the whole human TFIIH core structure, which indicates that the PH-D moves around the surface of core with a specific but limited spatial distribution; these dynamic structures were refined by molecular dynamics (MD) simulations. Furthermore, we built models, also refined by MD simulations, of TFIIH in complex with five p62-binding partners, including transcription factors TFIIEα, p53 and DP1, and nucleotide excision repair factors XPC and UVSSA. The models explain why the PH-D is crucially targeted by these factors, which use their intrinsically disordered acidic regions for TFIIH recruitment.
- Published
- 2020
6. Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways
- Author
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Chaowan Guo, Yoshifumi Nishimura, Tomoo Ogi, Yuka Nakazawa, and Masahiko Okuda
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0301 basic medicine ,Models, Molecular ,DNA Repair ,DNA repair ,Protein domain ,RNA polymerase II ,Biology ,medicine.disease_cause ,03 medical and health sciences ,Protein Domains ,Structural Biology ,Genetics ,medicine ,Humans ,Amino Acid Sequence ,Mutation ,Binding Sites ,Sequence Homology, Amino Acid ,T-cell receptor ,DNA ,Cell biology ,Pleckstrin homology domain ,DNA-Binding Proteins ,030104 developmental biology ,HEK293 Cells ,Transcription factor II H ,biology.protein ,Carrier Proteins ,Transcription Factor TFIIH ,Nucleotide excision repair ,DNA Damage ,Protein Binding - Abstract
Nucleotide excision repair is initiated by two different damage recognition subpathways, global genome repair (GGR) and transcription-coupled repair (TCR). In GGR, XPC detects DNA lesions and recruits TFIIH via interaction with the pleckstrin homology (PH) domain of TFIIH subunit p62. In TCR, an elongating form of RNA Polymerase II detects a lesion on the transcribed strand and recruits TFIIH by an unknown mechanism. Here, we found that the TCR initiation factor UVSSA forms a stable complex with the PH domain of p62 via a short acidic string in the central region of UVSSA, and determined the complex structure by NMR. The acidic string of UVSSA binds strongly to the basic groove of the PH domain by inserting Phe408 and Val411 into two pockets, highly resembling the interaction mechanism of XPC with p62. Mutational binding analysis validated the structure and identified residues crucial for binding. TCR activity was markedly diminished in UVSSA-deficient cells expressing UVSSA mutated at Phe408 or Val411. Thus, a common TFIIH recruitment mechanism is shared by UVSSA in TCR and XPC in GGR.
- Published
- 2017
7. The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH
- Author
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Kiyoshi Ohtani, Masahiko Okuda, Keigo Araki, and Yoshifumi Nishimura
- Subjects
Models, Molecular ,0301 basic medicine ,endocrine system ,Protein Conformation ,Protein subunit ,Biology ,Crystallography, X-Ray ,03 medical and health sciences ,Transactivation ,Structural Biology ,Protein Interaction Mapping ,Humans ,E2F1 ,Molecular Biology ,Transcription factor ,Acidic Region ,030102 biochemistry & molecular biology ,Cell Cycle ,Cell biology ,Pleckstrin homology domain ,030104 developmental biology ,Gene Expression Regulation ,Biochemistry ,Transcription factor II H ,biological phenomena, cell phenomena, and immunity ,Transcription factor II D ,Transcription Factor DP1 ,Transcription Factor TFIIH ,Protein Binding - Abstract
The heterodimeric transcription factor E2F1-DP1 plays crucial roles in coordinating gene expression during G1/S cell cycle progression. For transcriptional activation, the transactivation domain (TAD) of E2F1 is known to interact with the TATA-binding protein of TFIID and the p62 subunit of TFIIH. It is generally believed that DP1 facilitates E2F1 binding to target DNA and does not possess a TAD. Here, we show that an acidic region of DP1, whose function has remained elusive, binds to the plekstrin homology (PH) domain of p62 with higher affinity than that of E2F1 and contributes to transcriptional activation. The structure of the complex revealed that DP1 forms a twisted U-shaped, string-like conformation and binds to the surface of the PH domain by anchoring Phe403 into a pocket in the PH domain. The transcriptional activity of E2F1-DP1 was reduced when Phe403 of DP1 was mutated. These findings indicate that the acidic region of DP1 acts as a TAD by contacting TFIIH.
- Published
- 2016
8. Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH
- Author
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Masahiko Okuda, Tadashi Komatsu, Junichi Higo, Kenji Sugase, Tsuyoshi Konuma, and Yoshifumi Nishimura
- Subjects
0301 basic medicine ,Protein subunit ,Biophysics ,Molecular Dynamics Simulation ,010402 general chemistry ,Antiparallel (biochemistry) ,01 natural sciences ,Protein Structure, Secondary ,Transcription Factors, TFII ,03 medical and health sciences ,Molecular dynamics ,Protein Domains ,Humans ,Amino Acid Sequence ,Nuclear Magnetic Resonance, Biomolecular ,Alanine ,Acidic Region ,Chemistry ,Proteins ,0104 chemical sciences ,Pleckstrin homology domain ,Crystallography ,030104 developmental biology ,Mutation ,Transcription factor II H ,Transcription factor II E ,Hydrophobic and Hydrophilic Interactions ,Transcription Factor TFIIH ,Algorithms ,Protein Binding - Abstract
General transcription factor II E (TFIIE) contains an acid-rich region (residues 378–393) in its α -subunit, comprising 13 acidic and two hydrophobic (Phe387 and Val390) residues. Upon binding to the p62 subunit of TFIIH, the acidic region adopts an extended string-like structure on the basic groove of the pleckstrin homology domain (PHD) of p62, and inserts Phe387 and Val390 into two shallow pockets in the groove. Here, we have examined the dynamics of this interaction by NMR and molecular dynamics (MD) simulations. Although alanine substitution of Phe387 and/or Val390 greatly reduced binding to PHD, the binding mode of the mutants was similar to that of the wild-type, as judged by the chemical-shift changes of the PHD. NMR relaxation dispersion profiles of the interaction exhibited large amplitudes for residues in the C-terminal half-string in the acidic region (Phe387, Glu388, Val390, Ala391, and Asp392), indicating a two-site binding mode: one corresponding to the final complex structure, and one to an off-pathway minor complex. To probe the off-pathway complex structure, an atomically detailed free-energy landscape of the binding mode was computed by all-atom multicanonical MD. The most thermodynamically stable cluster corresponded to the final complex structure. One of the next stable clusters was the off-pathway structure cluster, showing the reversed orientation of the C-terminal half-string on the PHD groove, as compared with the final structure. MD calculations elucidated that the C-terminal half-acidic-string forms encounter complexes mainly around the positive groove region with nearly two different orientations of the string, parallel and antiparallel to the final structure. Interestingly, the most encountered complexes exhibit a parallel-like orientation, suggesting that the string has a tendency to bind around the groove in the proper orientation with the aid of Phe387 and/or Val390 to proceed smoothly to the final complex structure.
- Published
- 2016
9. Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC
- Author
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Kaoru Sugasawa, Yoshifumi Nishimura, Minoru Kinoshita, Erina Kakumu, and Masahiko Okuda
- Subjects
Models, Molecular ,DNA Repair ,Ultraviolet Rays ,DNA damage ,DNA repair ,Molecular Sequence Data ,Gene Expression ,Saccharomyces cerevisiae ,Biology ,Crystallography, X-Ray ,medicine.disease_cause ,Protein Structure, Secondary ,Cell Line ,chemistry.chemical_compound ,Structural Biology ,Escherichia coli ,medicine ,Humans ,Amino Acid Sequence ,Molecular Biology ,Mutation ,Binding Sites ,DNA ,Fibroblasts ,Molecular biology ,Recombinant Proteins ,Protein Structure, Tertiary ,Cell biology ,DNA-Binding Proteins ,Pleckstrin homology domain ,Kinetics ,Protein Subunits ,Transcription Factor TFIIH ,chemistry ,Transcription factor II H ,Peptides ,DNA Damage ,Protein Binding ,Nucleotide excision repair - Abstract
SummaryIn global genome repair (GGR), XPC detects damaged nucleotides and recruits TFIIH complex. The small acidic region of XPC binds to the pleckstrin homology (PH) domain of TFIIH subunit p62; however, the recognition mechanism remains elusive. Here, we use nuclear magnetic resonance to present the tertiary structure of XPC bound to the PH domain. The XPC acidic region forms a long string stabilized by insertion of Trp133 and Val136 into two separate hollows of the PH domain, coupled with extensive electrostatic contacts. Analysis of several XPC mutants revealed that particularly Trp133 is essential for binding to the PH domain. In cell lines stably expressing mutant XPC, alanine substitution at Trp133 or Trp133/Val136 compromised UV resistance, recruitment of TFIIH to DNA damage, and removal of UV-induced photoproducts from genomic DNA. These findings show how TFIIH complex is recruited by XPC to damaged DNA, advancing our understanding of the early stage of GGR.
- Published
- 2015
10. The Eaf3 chromodomain acts as a pH sensor for gene expression by altering its binding affinity for histone methylated-lysine residues.
- Author
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Masahiko Okuda and Yoshifumi Nishimura
- Subjects
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HISTONES , *GENE expression , *RNA polymerases , *RNA polymerase II , *GENETIC regulation , *HISTONE acetylation , *HISTONE acetyltransferase - Abstract
During gene expression, histone acetylation by histone acetyltransferase (HAT) loosens the chromatin structure around the promoter to allow RNA polymerase II (Pol II) to initiate transcription, while de-acetylation by histone deacetylase (HDAC) tightens the structure in the transcribing region to repress false initiation. Histone acetylation is also regulated by intracellular pH (pHi) with global hypoacetylation observed at low pHi, and hyperacetylation, causing proliferation, observed at high pHi. However, the mechanism underlying the pHi-dependent regulation of gene expression remains elusive. Here, we have explored the role of the chromodomain (CD) of budding yeast Eaf3, a common subunit of both HAT and HDAC that is thought to recognize methylated lysine residues on histone H3. We found that Eaf3 CD interacts with histone H3 peptides methylated at Lys4 (H3K4me, a promoter epigenetic marker) and Lys36 (H3K36me, a coding region epigenetic marker), as well as with many dimethyl-lysine peptides and even arginine-asymmetrically dimethylated peptides, but not with unmethylated, phosphorylated or acetylated peptides. The Eaf3 CD structure revealed an unexpected histidine residue in the aromatic cage essential for binding H3K4me and H3K36me. pH titration experiments showed that protonation of the histidine residue around physiological pH controls the charge state of the aromatic cage to regulate binding to H3K4me and H3K36me. Histidine substitution and NMR experiments confirmed the correlation of histidine pKa with binding affinity. Collectively, our findings suggest that Eaf3 CD functions as a pHi sensor and a regulator of gene expression via its pHi-dependent interaction with methylated nucleosomes. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
11. Potential of a combined nitritation/anammox process using fixed-bed reactors for nitrogen removal from reject water in a municipal wastewater treatment plant
- Author
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Masahiko Okuda, Keita Takaki, Hiroki Itokawa, Hitoshi Nakazawa, and Kenji Furukawa
- Subjects
Waste management ,Wastewater ,Fixed bed ,Anammox ,Scientific method ,Environmental science ,Nitrogen removal - Published
- 2012
12. Nitrogen Removal from Anaerobic Digestion Supernatant using Fixed-bed Anammox Reactor
- Author
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Masahiko Okuda, Keita Takaki, Hiroki Itokawa, Hitoshi Nakazawa, and Kenji Furukawa
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Anaerobic digestion ,Chromatography ,Fixed bed ,Anammox ,Chemistry ,Nitrogen removal - Published
- 2011
13. Novel Structural and Functional Mode of a Knot Essential for RNA Binding Activity of the Esa1 Presumed Chromodomain
- Author
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Yoshifumi Nishimura, Norihiko Sano, Masahiko Okuda, Masami Horikoshi, Yoshihito Moriwaki, and Hideaki Shimojo
- Subjects
Models, Molecular ,Saccharomyces cerevisiae Proteins ,Tudor domain ,Protein Conformation ,Molecular Sequence Data ,Saccharomyces cerevisiae ,Biology ,Chromodomain ,chemistry.chemical_compound ,Protein structure ,Acetyltransferases ,Structural Biology ,Animals ,Nuclear Magnetic Resonance, Biomolecular ,Molecular Biology ,RNA-Binding Proteins ,RNA ,Methylated histone binding ,Histone acetyltransferase ,Recombinant Proteins ,chemistry ,Biochemistry ,biology.protein ,DNA ,Protein Binding ,Binding domain - Abstract
Chromodomains are methylated histone binding modules that have been widely studied. Interestingly, some chromodomains are reported to bind to RNA and/or DNA, although the molecular basis of their RNA/DNA interactions has not been solved. Here we propose a novel binding mode for chromodomain-RNA interactions. Essential Sas-related acetyltransferase 1 (Esa1) contains a presumed chromodomain in addition to a histone acetyltransferase domain. We initially determined the solution structure of the Esa1 presumed chromodomain and showed it to consist of a well-folded structure containing a five-stranded beta-barrel similar to the tudor domain rather than the canonical chromodomain. Furthermore, the domain showed no RNA/DNA binding ability. Because the N-terminus of the protein forms a helical turn, we prepared an N-terminally extended construct, which we surprisingly found to bind to poly(U) and to be critical for in vivo function. This extended protein contains an additional beta-sheet that acts as a knot for the tudor domain and binds to oligo(U) and oligo(C) with greater affinity compared with other oligo-RNAs and DNAs examined thus far. The knot does not cause a global change in the core structure but induces a well-defined loop in the tudor domain itself, which is responsible for RNA binding. We made 47 point mutants in an esa1 mutant gene in yeast in which amino acids of the Esa1 knotted tudor domain were substituted to alanine residues and their functional abilities were examined. Interestingly, the knotted tudor domain mutations that were lethal to the yeast lost poly(U) binding ability. Amino acids that are related to RNA interaction sites, as revealed by both NMR and affinity binding experiments, are found to be important in vivo. These findings are the first demonstration of how the novel structure of the knotted tudor domain impacts on RNA binding and how this influences in vivo function.
- Published
- 2008
14. Development of Intelligent Prosthetic Knee Joint
- Author
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Masahiko Okuda, Yoshihiro Kodama, and Tsutomu Togashi
- Subjects
Computer science ,Human–computer interaction ,Mechanical Engineering ,Prosthetic knee ,Robot ,Joint (building) ,User oriented - Published
- 2007
15. Structural Insights into the Asymmetric Effects of Zinc-Ligand Cysteine Mutations in the Novel Zinc Ribbon Domain of Human TFIIEα for Transcription
- Author
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Masahiko Okuda, Yoshifumi Nishimura, Fumio Hanaoka, Yoshiaki Ohkuma, and Aki Tanaka
- Subjects
Models, Molecular ,Protein Conformation ,Stereochemistry ,Mutant ,chemistry.chemical_element ,RNA polymerase II ,Zinc ,Ligands ,Biochemistry ,Protein Structure, Secondary ,Transcription Factors, TFII ,Protein structure ,Animals ,Humans ,Cysteine ,Molecular Biology ,Zinc finger ,Sequence Homology, Amino Acid ,biology ,General transcription factor ,Zinc Fingers ,General Medicine ,Magnetic Resonance Imaging ,Crystallography ,chemistry ,Mutation ,biology.protein ,RNA Polymerase II ,Transcription factor II E - Abstract
The large subunit of TFIIE (TFIIEalpha) has a highly conserved zinc ribbon domain, which is essential for transcription. Recently, we determined the solution structure of this domain to be that of a novel zinc finger motif [Okuda et al. (2004) J. Biol. Chem. 279, 51395-51403]. On examination of the functions of four cysteine mutants of TFIIEalpha, in which each of four zinc-liganded cysteines was replaced by alanine, we found an interesting functional asymmetry; on a supercoiled template, the two C-terminal mutants did not show any transcriptional activity, however, the two N-terminal mutants retained about 20% activity. Furthermore, these two pairs of mutants showed distinct binding abilities as to several general transcription factors. To obtain structural insights into the asymmetry, here we have analyzed the structures of the four cysteine mutants of the zinc ribbon domain by CD and NMR. All four mutants possessed a characteristic partially folded structure coordinating with a zinc atom, despite the imperfect set of cysteine-ligands. However, they equilibrated with several structures including the random coil structure. Unexpectedly, the two N-terminal mutants mainly equilibrated with the random coil structure, while the two C-terminal ones mainly equilibrated with folded structures. The characteristic structure formation of each mutant was reversible, which totally depended on the zinc binding.
- Published
- 2005
16. Investigation of molecular size of transcription factor TFIIE in solution
- Author
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Satoko Akashi, Satoru Unzai, Yoshiyuki Itoh, Mamoru Sato, Aritaka Nagadoi, Masahiko Okuda, and Yoshifumi Nishimura
- Subjects
Spectrometry, Mass, Electrospray Ionization ,Recombinant Fusion Proteins ,Electrospray ionization ,Amino Acid Motifs ,Molecular Sequence Data ,RNA polymerase II ,Biochemistry ,Transcription Factors, TFII ,Structural Biology ,Transcription (biology) ,Humans ,Scattering, Radiation ,Molecular Biology ,Chromatography ,biology ,Molecular mass ,General transcription factor ,Chemistry ,Heterotetramer ,Molecular Weight ,Solutions ,Transcription preinitiation complex ,Chromatography, Gel ,biology.protein ,Biophysics ,RNA Polymerase II ,Transcription factor II E ,Ultracentrifugation - Abstract
Human general transcription factor IIE (TFIIE), a component of a transcription preinitiation complex associated with RNA polymerase II, was characterized by size-exclusion chromatography, mass spectrometry, analytical ultracentrifugation, and small-angle X-ray scattering (SAXS). Recombinant human TFIIE was purified to homogeneity and shown to contain equimolar amounts of TFIIEα (50 kDa) and TFIIEβ (35 kDa) by SDS-PAGE. In the analysis of size-exclusion chromatography of the purified sample, as already reported, TFIIE was shown to be a 170-kDa α2β2 heterotetramer. However, by using electrospray ionization mass spectrometry the purified sample gave the molecular mass of 84,152 ± 5, indicating that TFIIE is an αβ heterodimer but not a heterotetramer. Analytical ultracentrifugation experiment of TFIIE provided that only a single component with the molecular mass of ca. 80,000 existed in solution, also suggesting an αβ heterodimer. In addition, its extraordinarily rod-like molecular shape was confirmed by SAXS. It is likely that the rod-like molecular shape of TFIIE has misled larger molecular size in size-exclusion chromatography, which was calibrated by globular proteins. It is demonstrated that TFIIE exists as a heterodimer under our present conditions in solution, although two molecules of heterodimer might be required for the formation of the preinitiation complex with RNA polymerase II for starting the transcription process. Proteins 2005. © 2005 Wiley-Liss, Inc.
- Published
- 2005
17. A Novel Zinc Finger Structure in the Large Subunit of Human General Transcription Factor TFIIE
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Yoko Arai, Masahiko Okuda, Yoshiaki Ohkuma, Aritaka Nagadoi, Fumio Hanaoka, Manami Satoh, Aki Tanaka, Hideyasu Okamura, and Yoshifumi Nishimura
- Subjects
Models, Molecular ,Magnetic Resonance Spectroscopy ,Transcription, Genetic ,Protein Conformation ,Amino Acid Motifs ,Molecular Sequence Data ,Biology ,Ligands ,Biochemistry ,Protein Structure, Secondary ,Transcription Factors, TFII ,Escherichia coli ,Humans ,Point Mutation ,Amino Acid Sequence ,Cysteine ,Molecular Biology ,RNA polymerase II holoenzyme ,DNA Primers ,Glutathione Transferase ,Zinc finger ,Alanine ,Sequence Homology, Amino Acid ,General transcription factor ,Zinc Fingers ,Cell Biology ,Molecular biology ,Recombinant Proteins ,Protein Structure, Tertiary ,Cell biology ,Zinc ,Mutation ,Transcription preinitiation complex ,Mutagenesis, Site-Directed ,Transcription factor II H ,Electrophoresis, Polyacrylamide Gel ,Transcription factor II E ,Transcription factor II B ,Transcription factor II A ,Plasmids ,Protein Binding - Abstract
The zinc finger domain in the large subunit of TFIIE (TFIIEalpha) is phylogenetically conserved and is essential for transcription. Here, we determined the solution structure of this domain by using NMR. It consisted of one alpha-helix and five beta-strands, showing novel features distinct from previously determined zinc-binding structures. We created point mutants of TFIIEalpha in this domain and examined their binding abilities to other general transcription factors as well as their transcription activities. Four Zn(2+)-ligand mutants, in which each of cysteine residues at positions 129, 132, 154, and 157 was replaced by alanine, possessed no transcription activities on a linearized template, whereas, on a supercoiled template, interesting functional asymmetry was observed: although the C-terminal two mutants abolished transcription activity (5%), the N-terminal two mutants retained about 20% activities. The N-terminal two mutants bound stronger to the small subunit of TFIIF than the wild type and the C-terminal two mutants were impaired in their binding abilities to the XPB subunits of TFIIH. These suggest that the structural integrity of the zinc finger domain is essential for the TFIIE function, particularly in the transition from the transcription initiation to elongation and the conformational tuning of this domain for appropriate positioning of TFIIF, TFIIH, and polymerase II would be needed depending on the situation and timing.
- Published
- 2004
18. Extended string binding mode of the phosphorylated transactivation domain of tumor suppressor p53
- Author
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Yoshifumi Nishimura and Masahiko Okuda
- Subjects
Models, Molecular ,Chemistry ,Protein subunit ,RNA-Binding Proteins ,RNA-binding protein ,General Chemistry ,Plasma protein binding ,Biochemistry ,Catalysis ,Protein Structure, Secondary ,Protein Structure, Tertiary ,Pleckstrin homology domain ,Transactivation ,Colloid and Surface Chemistry ,Protein structure ,Mutation ,Transcription factor II H ,Biophysics ,Phosphorylation ,Humans ,Tumor Suppressor Protein p53 ,Protein Binding - Abstract
The transactivation domain (TAD) of tumor suppressor p53 has homologous subdomains, TAD1 and TAD2. Both are intrinsically disordered in their free states, but all structures of TAD1 and TAD2 bound to their target proteins have demonstrated use of an amphipathic α-helix, suggesting that the binding-coupled helix folding mechanism of TAD1 and TAD2 is essential. Although phosphorylation of TAD is important to switch the function of p53, bound structures of phosphorylated TAD1 and TAD2 have not been determined. Here, we reveal the recognition mechanism of the phosphorylated TAD2 bound to a pleckstrin homology (PH) domain from human TFIIH subunit p62 in an extended string-like conformation. This string-like binding mode of TAD2 seems to be independent of its phosphorylation in spite of enhanced binding activity upon phosphorylation. This is in contrast to the amphipathic helical binding mode of the unphosphorylated TAD2 to the yeast tfb1 PH domain and demonstrates that the p53 TAD2 has much higher conformational malleability than previously appreciated.
- Published
- 2014
19. Overexpression in Escherichia coli of Chemically Synthesized Gene for Active 0.19 -Amylase Inhibitor from Wheat Kernel1
- Author
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Takanori Satoh, Nobuhiko Sakurai, Masahiko Okuda, Tatsuya Samejima, Hiroyuki Kaji, and Kazunori Shibuya
- Subjects
Alpha amylase inhibitor ,General Medicine ,Biology ,medicine.disease_cause ,Biochemistry ,Molecular biology ,Inclusion bodies ,law.invention ,Gene product ,Open reading frame ,law ,Recombinant DNA ,medicine ,Molecular Biology ,Gene ,Escherichia coli ,Peptide sequence - Abstract
A synthetic gene encoding 0.19 alpha-amylase inhibitor (alpha-AI) from wheat kernel was obtained by enzymatic assembly of 18 oligodeoxynucleotides which were chemically synthesized. The synthetic gene was introduced into vector pET15b for expression in Escherichia coli BL21(DE3) under the control of T7 promoter. However, in SDS-PAGE and Western blotting analyses of the E. coli cell lysate, the expression product could not be detected. Expression analysis for various partially deleted gene fragments suggested that the putative hairpin-like structure of mRNA in the 5'-terminal coding region might interrupt efficient expression. When the hairpin structure was eliminated by using degenerate codons, the resulting gene could be overexpressed in E. coli. Although the gene product was accumulated in an insoluble fraction as inclusion bodies, its inhibitory activity could be recovered by solubilization with 8 M urea, followed by refolding through two successive steps of dialysis at alkaline pH. After purification, the recombinant 0.19 alpha-AI showed the same characteristics as the authentic inhibitor in terms of N-terminal amino acid sequence, peptide mapping on reverse-phase HPLC, far-UV circular dichroism (CD) spectrum and have inhibition of human salivary alpha-amylase. Thus, we have established an overexpression system in E. coli for active recombinant 0.19 alpha-AI.
- Published
- 1997
20. Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.
- Author
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Masahiko Okuda, Yuka Nakazawa, Chaowan Guo, Tomoo Ogi, and Yoshifumi Nishimura
- Published
- 2017
- Full Text
- View/download PDF
21. [Structural biology of a general transcription factor, TFIIE and its interaction mode with TFIIH]
- Author
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Masahiko, Okuda and Yoshifumi, Nishimura
- Subjects
Transcription Factors, TFII ,Binding Sites ,Humans ,Tumor Suppressor Protein p53 ,Transcription Factor TFIIH ,Protein Binding ,Protein Structure, Tertiary - Published
- 2008
22. Structural characterization of human general transcription factor TFIIF in solution
- Author
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Seiji Yamamoto, Yoshiaki Ohkuma, Satoko Akashi, Shinjiro Nagakura, Masahiko Okuda, and Yoshifumi Nishimura
- Subjects
Spectrometry, Mass, Electrospray Ionization ,Chromatography ,biology ,General transcription factor ,RNA polymerase II ,Biochemistry ,Recombinant Proteins ,Article ,Solutions ,chemistry.chemical_compound ,Transcription Factors, TFII ,Cross-Linking Reagents ,chemistry ,Transcription (biology) ,biology.protein ,Chromatography, Gel ,Humans ,Transcription factor II F ,Transcription factor II E ,Molecular Biology ,Transcription factor ,Dimerization ,Transcription factor II A ,DNA - Abstract
Human general transcription factor IIF (TFIIF), a component of the transcription pre-initiation complex (PIC) associated with RNA polymerase II (Pol II), was characterized by size-exclusion chromatography (SEC), electrospray ionization mass spectrometry (ESI-MS), and chemical cross-linking. Recombinant TFIIF, composed of an equimolar ratio of alpha and beta subunits, was bacterially expressed, purified to homogeneity, and found to have a transcription activity similar to a natural one in the human in vitro transcription system. SEC of purified TFIIF, as previously reported, suggested that this protein has a size200 kDa. In contrast, ESI-MS of the purified sample gave a molecular size of 87 kDa, indicating that TFIIF is an alphabeta heterodimer, which was confirmed by matrix-assisted laser desorption/ionization (MALDI) MS of the cross-linked TFIIF components. Recent electron microscopy (EM) and photo-cross-linking studies showed that the yeast TFIIF homolog containing Tfg1 and Tfg2, corresponding to the human alpha and beta subunits, exists as a heterodimer in the PIC, so the human TFIIF is also likely to exist as a heterodimer even in the PIC. In the yeast PIC, EM and photo-cross-linking studies showed different results for the mutual location of TFIIE and TFIIF along DNA. We have examined the direct interaction between human TFIIF and TFIIE by ESI-MS, SEC, and chemical cross-linking; however, no direct interaction was observed, at least in solution. This is consistent with the previous photo-cross-linking observation that TFIIF and TFIIE flank DNA separately on both sides of the Pol II central cleft in the yeast PIC.
- Published
- 2008
23. Effects of cage widths and depths for growing stage on egg laying type chicks and on their subsequent performance
- Author
-
Kyo Kondo, Takahiko Kawamura, Masahiko Okuda, and Kazuo Hirose
- Subjects
Animal science ,Stage (hydrology) ,Biology ,Cage ,Egg laying - Abstract
採卵鶏の育成用ケージについて,異なる大きさのケージを用いて検討した。間口を90cm, 67.5cm,45cm,奥行を60cm, 45cm, 30cmとした高さ45cmの9種類のケージを使い,飼育密度を450cm2/羽に一定として,1ケージ当たり3~12羽を収容した。7週齢より19週齢まで育成したが,10週齢からは飼料を自由摂取するものと制限給餌するものに2分した。なお,90cm×60cmのケージに8羽を収容し,従来の飼育密度675cm2/羽として育成した鶏を対照とした。その結果,雛の発育はケージの間口よりも奥行によって生じる影響の大きいことが知られた。自由摂取により奥行30cmのケージで育成した鶏の20週齢体重は60cmケージの場合より大きく,制限給餌による育成ではケージ奥行による平均体重の差は認められなかったが,個体差が小さくなり斉一化された。悪癖による被害も奥行30cmのケージにおける発生が少なかった。育成した鶏の産卵,卵重,飼料摂取量,飼料要求率,体重及び生存率を60週齢まで調べたが,育成方式による差は認められなかった。
- Published
- 1990
24. Real-time and simultaneous monitoring of the phosphorylation and enhanced interaction of p53 and XPC acidic domains with the TFIIH p62 subunit
- Author
-
Masahiko Okuda and Yoshifumi Nishimura
- Subjects
inorganic chemicals ,Cancer Research ,Kinase ,Biology ,environment and public health ,Phosphorylation cascade ,Pleckstrin homology domain ,Serine ,enzymes and coenzymes (carbohydrates) ,Transcription Factor TFIIH ,Biochemistry ,bacteria ,Phosphorylation ,Original Article ,Protein phosphorylation ,Threonine ,Molecular Biology - Abstract
Posttranslational modifications have critical roles in diverse biological processes through interactions. Tumor-suppressor protein p53 and nucleotide excision repair factor XPC each contain an acidic region, termed the acidic transactivation domain (TAD) and acidic fragment (AF), respectively, that binds to the pleckstrin homology (PH) domain of the p62 subunit of the transcription factor TFIIH. Human p53-TAD contains seven serine and two threonine residues, all of which can be phosphorylated. Similarly, XPC-AF contains six serine and two threonine residues, of which Thr117, Ser122 and Ser129 have been reported as phosphorylation sites in vivo, although their phosphorylation roles are unknown. Phosphorylation of Ser46 and Thr55 of p53-TAD increases its binding ability; however, the role of XPC-AF phosphorylation remains elusive. Here we describe a system for real-time and simultaneous monitoring of the phosphorylation and p62-PH affinity of p53-TAD and XPC-AF using nuclear magnetic resonance (NMR) spectroscopy. Unexpectedly, among seven reported kinases that presumably phosphorylate Ser46 and/or Thr55 of p53-TAD, only two specific and high-efficiency enzymes were identified: JNK2α2 for Ser46 and GRK5 for Thr55. During interaction with p62-PH, four different affinity complexes resulting from various phosphorylation states of p53-TAD by the kinases were identified. The kinetics of the site-specific phosphorylation reaction of p53-TAD and its affinity for p62-PH were monitored in real-time using the NMR system. Isothermic calorimetry showed that phosphorylation of Ser129 of XPC-AF increases binding to p62-PH. Although CK2 was predicted to phosphorylate Ser122, Ser129 and Ser140 from its sequence context, it specifically and efficiently phosphorylated only Ser129. Simultaneous monitoring of the phosphorylation and augmentation in p62-PH binding identified a key residue of p62-PH for contacting phosphorylated Ser129. In summary, we have established an NMR system for real-time and simultaneous monitoring of site-specific phosphorylation and enhancement of affinity between phosphorylation domains and their target. The system is also applicable to other posttranslational modifications.
- Published
- 2015
25. Structural polymorphism of chromodomains in Chd1
- Author
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Yoshifumi Nishimura, Masami Horikoshi, and Masahiko Okuda
- Subjects
Saccharomyces cerevisiae Proteins ,Protein Conformation ,Molecular Sequence Data ,Molecular Conformation ,Chromatin remodeling ,Protein Structure, Secondary ,Chromodomain ,Histones ,Histone H3 ,Structural Biology ,Histone methylation ,Humans ,Amino Acid Sequence ,Molecular Biology ,Protein secondary structure ,Polymorphism, Genetic ,biology ,Sequence Homology, Amino Acid ,Lysine ,DNA Helicases ,DNA Methylation ,Protein tertiary structure ,Protein Structure, Tertiary ,DNA-Binding Proteins ,Histone ,Biochemistry ,biology.protein ,Heterochromatin protein 1 - Abstract
Chromodomain from heterochromatin protein 1 and polycomb protein is known to be a lysine-methylated histone H3 tail-binding module. Chromo-helicase/ATPase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodeling factor, containing two tandem chromodomains. In human CHD1, both chromodomains are essential for specific binding to a K4 methylated histone H3 (H3 MeK4) peptide and are found to bind cooperatively in the crystal structure. For the budding yeast homologue, Chd1, the second but not the first chromodomain was once reported to bind to an H3 MeK4 peptide. Here, we reveal that neither the second chromodomain nor a region containing tandem chromodomains from yeast Chd1 bind to any lysine-methylated or arginine-methylated histone peptides that we examined. In addition, we examined the structures of the chromodomains from Chd1 by NMR. Although the tertiary structure of the region containing tandem chromodomains could not be obtained, the secondary structure deduced from NMR is well conserved in the tertiary structures of the corresponding first and second chromodomains determined individually by NMR. Both chromodomains of Chd1 demonstrate a structure similar to that of the corresponding part of CHD1, consisting of a three-stranded β-sheet followed by a C-terminal α-helix. However, an additional helix between the first and second β-strands, which is found in both of the first chromodomains of Chd1 and CHD1, is positioned in an entirely different manner in Chd1 and CHD1. In human CHD1 this helix forms the peptide-binding site. The amino acid sequences of the chromodomains could be well aligned on the basis of these structures. The alignment showed that yeast Chd1 lacks several key functional residues, which are responsible for specific binding to a methylated lysine residue in other chromodomains. Chd1 is likely to have no binding affinity for any H3 MeK peptide, as found in other chromodomain proteins.
- Published
- 2006
26. [Structural biology on transcription]
- Author
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Masahiko, Okuda and Yoshifumi, Nishimura
- Subjects
Cyclin H ,Transcription Factors, TFII ,Saccharomyces cerevisiae Proteins ,Transcription, Genetic ,Acetyltransferases ,Protein Conformation ,Cyclins ,Humans ,RNA Polymerase II ,Chromatin ,Histone Deacetylases ,Histone Acetyltransferases ,Protein Structure, Tertiary - Published
- 2002
27. Intelligent Prosthetic Knee Joint which Supports Lost Ability by Technologies
- Author
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Masahiko Okuda
- Subjects
medicine.medical_specialty ,Physical medicine and rehabilitation ,Computer science ,Prosthetic knee ,medicine ,Joint (building) - Published
- 2011
28. Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface
- Author
-
Yoshifumi Nishimura, Fumio Hanaoka, Yoshinori Watanabe, Hideyasu Okamura, Masahiko Okuda, and Yoshiaki Ohkuma
- Subjects
Models, Molecular ,Transcription, Genetic ,Molecular Sequence Data ,Static Electricity ,RNA polymerase II ,Winged Helix ,General Biochemistry, Genetics and Molecular Biology ,Chromatography, Affinity ,Protein Structure, Secondary ,Structure-Activity Relationship ,Transcription Factors, TFII ,Chymotrypsin ,Humans ,Trypsin ,Amino Acid Sequence ,Promoter Regions, Genetic ,Molecular Biology ,Nuclear Magnetic Resonance, Biomolecular ,Sequence Deletion ,Binding Sites ,General Immunology and Microbiology ,biology ,General transcription factor ,General Neuroscience ,Helix-Loop-Helix Motifs ,DNA ,Articles ,Molecular biology ,Peptide Fragments ,Protein Structure, Tertiary ,DNA-Binding Proteins ,Transcription preinitiation complex ,biology.protein ,Biophysics ,Transcription factor II E ,Transcription factor II D ,Transcription factor II B ,Sequence Alignment ,Transcription factor II A ,Transcription Factors - Abstract
Human general transcription factor TFIIE consists of two subunits, TFIIEalpha and TFIIEbeta. Recently, TFIIEbeta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. Here, the central core domain of human TFIIEbeta (TFIIEbetac) has been identified by a limited proteolysis. This solution structure has been determined by NMR. It consists of three helices with a beta hairpin at the C-terminus, resembling the winged helix proteins. However, TFIIEbetac shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow. A model will be proposed that TFIIE stabilizes the preinitiation complex by binding not only to the general transcription factors together with RNA polymerase II but also to the promoter DNA, where double-stranded DNA starts to open to be single-stranded upon activation of the preinitiation complex.
- Published
- 2000
29. Extended String Binding Mode of the Phosphorylated Transactivation Domain of Tumor Suppressor p53.
- Author
-
Masahiko Okuda and Yoshifumi Nishimura
- Subjects
- *
P53 protein , *PHOSPHORYLATION , *MOLECULAR recognition , *MOLECULAR conformation , *HOMOLOGY (Biochemistry) - Abstract
The transactivation domain (TAD) of tumor suppressor p53 has homologous subdomains, TAD1 and TAD2. Both are intrinsically disordered in their free states, but all structures of TAD1 and TAD2 bound to their target proteins have demonstrated use of an amphipathic α-helix, suggesting that the binding-coupled helix folding mechanism of TAD1 and TAD2 is essential. Although phosphorylation of TAD is important to switch the function of p53, bound structures of phosphorylated TAD1 and TAD2 have not been determined. Here, we reveal the recognition mechanism of the phosphorylated TAD2 bound to a pleckstrin homology (PH) domain from human TFIIH subunit p62 in an extended string-like conformation. This string-like binding mode of TAD2 seems to be independent of its phosphorylation in spite of enhanced binding activity upon phosphorylation. This is in contrast to the amphipathic helical binding mode of the unphosphorylated TAD2 to the yeast tfb1 PH domain and demonstrates that the p53 TAD2 has much higher conformational malleability than previously appreciated. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
30. Control of the composition of Y-Ba-Cu-O superconducting thin films deposited by RF diode sputtering
- Author
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Kouzou Nishimura, Hiroshi Kajikawa, Yoshio Kawate, Masahiko Okuda, and Takashi Hase
- Subjects
Materials science ,Mechanical Engineering ,Metals and Alloys ,Analytical chemistry ,Electron microprobe ,Partial pressure ,Electron ,Industrial and Manufacturing Engineering ,Sputtering ,Materials Chemistry ,Composition (visual arts) ,Thin film ,Power density ,Diode - Abstract
The composition of Y-Ba-Cu-O thin films deposited by RF diode sputtering was examined by EPMA (Electron Probe Micro Analysis). The composition of Y-Ba-Cu-O thin films with a target made by the solid state reaction method changed with sputtering time even if the films were deposited under identical conditions. In contrast, the composition of films with a target made by the co-precipitation method were unaffected by sputtering time when they were deposited under identical conditions. Good control of the composition of Y-Ba-Cu-O thin films was achieved by optimizing both the RF input power density and the partial pressure of oxygen.
- Published
- 1988
31. Non-equilibrium vapour condensation on a shock-tube endwall behind a reflected shock wave
- Author
-
Tomonobu Goto, Teruaki Akamatsu, Shigeo Fujikawa, and Masahiko Okuda
- Subjects
Shock wave ,Materials science ,Mechanical Engineering ,Condensation ,Thermodynamics ,Mechanics ,Condensed Matter Physics ,Method of matched asymptotic expansions ,Shock (mechanics) ,Mechanics of Materials ,Heat transfer ,Reflection (physics) ,Shock tube ,Intensity (heat transfer) - Abstract
This paper deals theoretically with a filmwise condensation of a vapour on the endwall of a shock tube behind a reflected shock wave. The gas dynamics, accompanied by heat and mass transfer at the vapour-liquid interface, is treated by the method of matched asymptotic expansions. The first and second approximate solutions are obtained and evaluated numerically. It is clarified that there exists a transition process on the growth of a liquid film, that is, the liquid film grows approximately in proportion to the time t in the early stages after the reflection of the shock wave, and after some time, it grows in proportion to the square root of the time. This transition process from the t-dependent growth to the t½-dependent one is mainly controlled by the intensity of condensation. In the t-dependent growth region, the growth rate of the liquid film is proportional to the condensation parameter, depending both upon an initial condition and upon thermal properties of the vapour and the liquid film, while in the t½-dependent growth region it becomes independent of the condensation parameter and is controlled only by thermal properties of the vapour, liquid film and shock-tube endwall. This result suggests that the measurement of the condensation parameter by shock tubes should be made in the t-dependent growth region immediately after the reflection of the shock wave.
- Published
- 1987
32. Study of Niobium Sputter-coating forSuperconducting Nb/Cu-cavities
- Author
-
Masahiko, OKUDA
- Abstract
本研究は高周波同軸マグネトロンスパッタ法により作製したNb膜の特性(特に高周波残留抵抗の発生の原因となるNb膜の柱状結晶組織)と成膜条件の関係を明らかにしたものである。さらには、電鋳法を用いたシームレスCu空洞の開発により、電鋳銅空洞にNbをスパッタ成膜したLバンド(I.5GHz、l.3GHz)Nb/Cu超伝導空洞が有用であることを実証した。 高周波空洞内に大きな電界をつくろうとすると、空洞壁をながれる高周波電流による損失が電界の2乗に比例して大きくなり、空洞壁を冷却することが難しくなるので、大きな高周波電力を供給できない。このために、常伝導空洞を用いたシンクロトロンでは最大加速電界が1.5MV/m程度に制限されており、リニアックでパルス運転を余儀なくされている。この問題を解決するために超伝導空洞が開発され、KEKでは1980年代後半にトリスタン主リング用508MHz超伝導空洞が世界にさきがけて実用化された。この超伝導空洞は、高加速電界が要求されるリニアコライダー、大電流のピーム加速が要求されるBファクトリーやニュートロンスパレーション用陽子リニアックなどに応用できる。また、高電界(大きな蓄積エネルギー)での運転により質の良いビームを得られることから、自由電子レーザーにも適しているしかし、理論から予測されるNb空洞の最大加速電界は、50~60MV/mであるのに対して、現状では10~30MV/mにとどまっている。この原因は、フィールドエミッシ∃ンや空洞壁での局部的な常電導転移による空洞のクエンチである。もう一つの問題点は製作コストが大きいことであり、製作コストそのものの削減に加えて、運転電界を上げることにより転位加速電界当たりのコストを下げることが要求されている。その対策として、表面処理の工夫により常伝導転移部の発生原因になる空洞表面の欠陥を少なくし、残留抵抗比が大きいNb材の使用により空洞壁の熱伝導度を大きくして発熱の放散を促す努力がなされている。もう一つの方法は熱伝導度が大きい銅を持ちいて空洞を作り、内面のスパッタ法を用いてNbを成膜する方法である。このNb/Cu空洞の利点は、以下のようにまとめることができる。a)空洞熱の熱伝導率が大きいために局部的な発熱に対して安定である。b)パイプ冷却が可能であるのクライオスタットの構造が簡単になる。c)他の高Tc材料(NbTi,NbN,Nb3Sn,YBaCuO)にも応用が可能である。 しかしながら、現状では残留抵抗が大きいためにQ値が低下するという問題がある。本論文では、これらの原因は膜中の不純物、ミクロな剥離、スパッタ膜特有の柱状結晶組織にあると考え、スパッタ法により作製したNb膜の特性と成膜条件の関係を把握することを主な目的とした。この試みは残留抵抗の発生源の究明につながり、Nb/Cu空洞の問題点の解決あるいは限界は見極める上で意義のあることである。 まず初めに、スパッタ法の基礎に立ち返り、Nb/Cu空洞の成膜方法と成膜条件について基礎的な検討を行った。スパッタ法の特徴は(蒸発法に比べて)、スパッタ原子が数~数100eVの比較的大きなエネルギーを持ていること、膜が数~数100eVのイオンや電子の衝撃を受けること、雰囲気に0.1から10Paの比較的高い圧力のガス分子が存在することである。この特徴を活かして高純度Nb膜を製作するには、高周波マグネトロンスパッタ法が有利であり、バックグラウンド圧、Arガス圧、成膜速度、基板温度が膜質に影響を与えると判断した。またスパッタ膜の形態ゾーンモデルから、Nb膜では低Arガス圧高基板温度(0.1~1Pa、300~500℃)で柱状結晶組織が著名なゾーンlから緻密なゾーンTに遷移すると予想した。 つぎに、上述の検討に基づき、高周波同軸マグネトロンスパッタ法を用いたNb/Cu空洞専用成膜装置を開発した。この成膜装置の特徴は、Lバンドシングル空洞に対して、低バックグラウンド圧(1X10-5~3×l0-5Pa、300℃)、高成膜速度(~1mm/s)で、広範囲の基板温度(100~450℃以上)、Arガス圧(0.1~15Pa)を設定できることにある。 つぎに、空洞内面に厚さが一様で高い密着性を持つNb膜を作製する方法について検討した。高Arガス圧では一様なNb膜を作製することができるが、低Arガス圧ではピームパイプ部のグロー放電が不安定になり成膜ができない。そこで高Arガス圧でピームパイプ部の成膜を行ったの地低Arガス圧で空洞部の成膜を行う方法と、磁石を移動させながら低Arガス圧で成膜する方法をとることで問題を回避できることを示した。また、成膜前に200から300℃で空洞を加熱することにより、液体窒素温度と室温間のヒートサイクルに対しても剥離のない高密着性のNb膜を得ることができる。しかし、温度が高すぎると膜表面にCuが拡散することが明らかになった。 つぎに、Nb膜の特性について調べた。到達圧カを10-5Pa以下にすると、Nb膜中の不純ガス成分量はNbバルクと同程度まで減少し、臨界温度はバルク以上の値を示した。この結果は、開発した成膜装置により不純物の少ないNb膜を作製できることを示している。高Arガス圧(1~10P)では膜の柱状結晶組織が著しくなりボイドが見られるのに対して、低Arガスでは膜が緻密になり、予想通り膜の形態がゾーンlからゾーンTに遷移することを確認した。柱状結晶組織の往の大きさが大きいゾーンlのNb膜ほど直流電気抵抗特性に優れており、柱が小さいゾーンTでは低下した。高周波特性は緻密で結晶粒界の結合が強いゾーンTの法が優れていると考えられるが、直流電気抵抗特性の測定結果は逆の傾向を示した。この結果から、直流残留抵抗と高周波残留抵抗の相違点に着目して、高周波残留抵抗の発生原因について考察した。ゾーンlでは基板のCu成分の表面拡散が多く、膜表面のCuが高周波残留抵抗の発生の原因になりえる。そこで、基板温度を上げることなしに電気特性に優れた緻密な膜を得る方法としてバイアススパッタを試み、空洞成膜への適用の可能性について検討した。最後に、Lバンド(1.5GHz,1.3GHz)Cu空洞にNb成膜を行い、Nb/Cu空洞の高周波超伝導特性を調べた。Cu空洞の製作では電鋳法を用いることで空洞部の溶接継ぎ目をなくし、電界研磨により鏡面仕上げを行った。この電鋳銅空洞の適用により、表面の欠陥による特性劣化の因子を無視できるようになった。Q測定値の結果、残留抵抗は大きい(~120nΩ)ながらも、フィールドエミッシ∃ンなしに最大10.4MV/m以上の加速電界を達成し、電鋳銅空洞にNbスパッタ成膜したNb/Cu超伝導空洞が有用であることを実証した。
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