Naoki Takaya, Seigo Kuwazaki, Yoshiaki Adachi, Sawako Suzuki, Tomoko Kikuchi, Hiro Nakamura, Yoshitsugu Shiro, Hirofumi Shoun,
... this author on: Oxford Academic PubMed Google Scholar Hiro Nakamura, Hiro Nakamura Search for other works by this author on: ...
Tópico(s): Algal biology and biofuel production
2003 - Oxford University Press | The Journal of Biochemistry
Koji Tamura, Hiro Nakamura, Yuji Tanaka, Soichi Oue, Koki Tsukamoto, Masaharu Nomura, Terumasa Tsuchiya, Shin‐ichi Adachi, Satoshi Takahashi, Tetsutarō Iizuka, Yoshitsugu Shiro,
... to Heme Iron in Oxygen Sensor FixLKoji Tamura, Hiro Nakamura, Yuji Tanaka, Soichi Oue, Koki Tsukamoto, Masaharu Nomura, ...
Tópico(s): Electrochemical sensors and biosensors
1996 - American Chemical Society | Journal of the American Chemical Society
Masahiro Mukai, Kayako Nakamura, Hiro Nakamura, Tetsutarō Iizuka, Yoshitsugu Shiro,
FixL is a sensor histidine kinase having a heme-containing domain as an O2 sensing site. In the study presented here, Ile209 and Ile210 located near the heme iron of the heme domain of Rhizobium meliloti FixL (RmFixL) were mutated, and the mutational effects on the regulation of the kinase activity and the heme pocket structure were examined by the autophosphorylation assay and UV−visible absorption and resonance Raman (RR) spectroscopies. The mutation of these residues disrupted the regulation of ...
Tópico(s): Diet, Metabolism, and Disease
2000 - American Chemical Society | Biochemistry
Satoru Akimoto, Atsunari Tanaka, Kayako Nakamura, Yoshitsugu Shiro, Hiro Nakamura,
FixL, a rhizobial heme-based O2-sensing histidine kinase, catalyzes autophosphorylation in the deoxy form at low O2 tension, while the kinase activity is inhibited in the case of the O2-bound form. The present study unambiguously shows that the binding of CO and NO does not significantly inhibit the kinase activity of dithiothreitol (DTT)-reduced ferrous FixL from Sinorhizobium meliloti, which is inconsistent with the spin state mechanism previously reported. Kinase inactivation is caused by aberrant ...
Tópico(s): Microbial Fuel Cells and Bioremediation
2003 - Elsevier BV | Biochemical and Biophysical Research Communications
Youichi Naoe, N. Nakamura, Akihiro Doi, Mia Sawabe, Hiro Nakamura, Yoshitsugu Shiro, Hiroshi Sugimoto,
Abstract Pathogenic bacteria remove iron from the haem of host tissues and use it as a catalytic center of many enzymes. Haem uptake by pathogenic bacteria is facilitated by the membrane-integrated haem importer, which belongs to the type II ATP-binding cassette (ABC) transporter. Here we present crystal structures of Burkholderia cenocepacia haem importer BhuUV complexed with the periplasmic haem-binding protein BhuT and in the absence of BhuT. The transmembrane helices of these structures show ...
Tópico(s): Hemoglobinopathies and Related Disorders
2016 - Nature Portfolio | Nature Communications
Ken Saito, Eiichi Ito, Kaito Hosono, Kayako Nakamura, Kiyohiro Imai, Tetsutarō Iizuka, Yoshitsugu Shiro, Hiro Nakamura,
Summary The rhizobial FixL/FixJ system, a member of the superfamily of bacterial two‐component signal transducing systems, regulates the expression of nitrogen fixation‐related genes by sensing environmental oxygen tension. Oxygen‐free (deoxy) FixL is autophosphorylated at an invariant histidine residue with ATP, and the phosphoryl group is transferred to FixJ, leading to an enhancement in transcriptional activity at low oxygen tensions, but the histidine kinase activity of the oxygen‐bound (oxy) ...
Tópico(s): Hemoglobin structure and function
2003 - Wiley | Molecular Microbiology
... with low concentration Co2+Hiroshi Endoh, Takaho Kaneko, Hiro Nakamura, Katsuhiko Doi, and Eiji Takahashi1 December 2000 | American ...
Tópico(s): PARP inhibition in cancer therapy
1992 - American Physiological Society | Physiological Reviews
Hiro Nakamura, Hiroshi Sasaki, Hisashi Hirano, Atushi Yamashita,
コムギ(Triticum aestivum L.)の日本および外国品種計376品種について,種子貯蔵蛋白質をドデシル硫酸ナトリウム-ポリアクリルアミトゲル電気泳動法によって分離した.その結果,外国品種には全く見られないグルテニンの高分子量145kDサブユニットが,日本品種に高頻度で認められた.このサブユニットは,電気泳動における移動度から,PAYNE et al.(1983)が報告したグルテニン2.2バンドと同一の蛋白質と推察された.コムギ農林登録131品種(コムギ農林1号~農林131号)では,約1/3の品種がこのサブユニットを有することが明らかとなった.また,グルテニン145kDサブユニットは,硬質・準硬質の品種に全く存在しないこと,中間質・軟質の品種では,高頻度で認められることがわかった.このことからこのサブユニットがコムギの硬軟質性と関連していると考えられた.また,遺伝分析の結果,グルテニン145kDサブユニットは,単一の遺伝子に支配されていることも明らかとなった.北海道・東北・北陸・長野など北日本の育成地で育成された品種の多くにこのサブユニットが存在せず,四国・九州など西日本で育成された品種の約3分の2がこの145kDサブユニットを保有していた. ...
Tópico(s): Phytase and its Applications
1990 - Japanese Society of Breeding | Ikushugaku zasshi
Shinsuke Kato, Hiro Nakamura, E Otomo,
Tópico(s): Bone and Dental Protein Studies
1989 - Springer Science+Business Media | Acta Neuropathologica
Gerardo G. Naumis, Saúl A. Herrera, Shiva Prasad Poudel, Hiro Nakamura, Salvador Barraza‐Lopez,
Abstract This is an update of a previous review (Naumis et al 2017 Rep. Prog. Phys. 80 096501). Experimental and theoretical advances for straining graphene and other metallic, insulating, ferroelectric, ferroelastic, ferromagnetic and multiferroic 2D materials were considered. We surveyed (i) methods to induce valley and sublattice polarisation ( P ) in graphene, (ii) time-dependent strain and its impact on graphene’s electronic properties, (iii) the role of local and global strain on superconductivity ...
Tópico(s): Ga2O3 and related materials
2023 - IOP Publishing | Reports on Progress in Physics
Hiro Nakamura, Tamao Hisano, MD Rahman, Takehiko Tosha, Mikako Shirouzu, Yoshitsugu Shiro,
Bacterial pathogens acquire heme from the host hemoglobin as an iron nutrient for their virulence and proliferation in blood. Concurrently, they encounter cytotoxic-free heme that escapes the heme-acquisition process. To overcome this toxicity, many gram-positive bacteria employ an ATP-binding cassette heme-dedicated efflux pump, HrtBA in the cytoplasmic membranes. Although genetic analyses have suggested that HrtBA expels heme from the bacterial membranes, the molecular mechanism of heme efflux ...
Tópico(s): Porphyrin Metabolism and Disorders
2022 - National Academy of Sciences | Proceedings of the National Academy of Sciences
Hong Jian Zhao, Hiro Nakamura, Rémi Arras, Charles Paillard, Peng Chen, Julien Gosteau, Li Xu, Yurong Yang, L. Bellaïche,
Purely cubic spin splittings in the band structure of bulk insulators have not been extensively investigated yet despite the fact that they may pave the way for novel spin-orbitronic applications and can also result in a variety of promising spin phenomena. By symmetry analysis and first-principles simulations, we report symmetry-enforced purely cubic spin splittings (SEPCSS) that can even lead to persistent spin textures. In particular, these SEPCSS can be thought to be complementary to the cubic ...
Tópico(s): Magnetic properties of thin films
2020 - American Physical Society | Physical Review Letters
Gareth S. A. Wright, Saeki Akane, Takaaki Hikima, Yoko Nishizono, Tamao Hisano, Misaki Kamaya, Kohei Nukina, Hideo Nishitani, Hiro Nakamura, Masaki Yamamoto, S.V. Antonyuk, S.S. Hasnain, Yoshitsugu Shiro, Hitomi Sawai,
Combined experimental and modeling techniques reveal the mechanism of signal relay in the oxygen-sensing FixL-FixJ two-component system.
Tópico(s): Fuel Cells and Related Materials
2018 - American Association for the Advancement of Science | Science Signaling
Seiji Yamada, Hiroshi Sugimoto, Miki Kobayashi, Ayako Ohno, Hiro Nakamura, Yoshitsugu Shiro,
We determined the structure of the complex of the sensory histidine kinase (HK) and its cognate response regulator (RR) in the two-component signal transduction system of Thermotoga maritima. This was accomplished by fitting the high-resolution structures of the isolated HK domains and the RR onto the electron density map (3.8 Å resolution) of the HK/RR complex crystal. Based on the structural information, we evaluated the roles of both interdomain and intermolecular interactions in the signal transduction ...
Tópico(s): Enzyme Structure and Function
2009 - Elsevier BV | Structure
Yoko Ito, Shoko Nakagawa, Ayako Komagata, Masao Ikeda-Saito, Yoshitsugu Shiro, Hiro Nakamura,
Corynebacterium diphteriae employs the response regulator, ChrA, and the sensor kinase, ChrS, of a two-component signal transduction system to utilize host heme iron. Although ChrS is predicted to encode a heme sensor, the sensing mechanism remains to be characterized. In this report, ChrS expressed in Eshcherichia coli membranes was solubilized and purified using decylmaltoside. ChrS protein incorporated into proteoliposomes catalyzed heme-dependent autophosphorylation by ATP. Other metalloporphyrins ...
Tópico(s): Lipid Membrane Structure and Behavior
2009 - Wiley | FEBS Letters
Eiji Kinoshita, Emiko Kinoshita‐Kikuta, Mamoru Matsubara, Seiji Yamada, Hiro Nakamura, Yoshitsugu Shiro, Yuri Aoki, Kouki Okita, Tohru Koike,
Herein, we demonstrate the separation of phosphoprotein isotypes having the same number of phosphate groups using phosphate-affinity SDS-PAGE. The phosphate-affinity site is a polyacrylamide-bound Phos-tag that enables the mobility shift detection of phosphoproteins from their nonphosphorylated counterparts. As the first practical example of the separation, we characterized the monophosphorylated Tau isotypes by each of three tyrosine kinases, c-Abl, MET, and Fyn. Each monophosphoisotype phosphorylated ...
Tópico(s): Enzyme Production and Characterization
2008 - Wiley | PROTEOMICS
Ryouta Takahashi, Koji Okajima, Hiroyuki Suzuki, Hiro Nakamura, Masahiko Ikeuchi, Takumi Noguchi,
The BLUF (sensor of blue light using FAD) domain is a blue light receptor possessing a flavin molecule as an active cofactor. A conserved Tyr residue located adjacent to flavin has been proposed to be a key amino acid in the mechanism of the photoreaction of the BLUF domain. We have studied the structure of this key Tyr residue and the relevance to the photoreaction in the BLUF protein of the cyanobacterium Thermosynechococcus elongatus, TePixD, by means of Fourier transform infrared (FTIR) difference ...
Tópico(s): Photosynthetic Processes and Mechanisms
2007 - American Chemical Society | Biochemistry
Seiji Yamada, Shuji Akiyama, Hiroshi Sugimoto, Hideyuki Kumita, Kazuki Ito, Tetsuro Fujisawa, Hiro Nakamura, Yoshitsugu Shiro,
Tópico(s): Protein Structure and Dynamics
2006 - Elsevier BV | Journal of Molecular Biology
Atsunari Tanaka, Hiro Nakamura, Yoshitsugu Shiro, Hiroshi Fujii,
FixL is a heme-based O(2) sensor, in which the autophosphorylation is regulated by the binding of exogenous ligands such as O(2) and CN(-). In this study, mutants of the heme distal Arg200, Arg208, Ile209, Ile210, and Arg214 residues of SmFixL were characterized biochemically and physicochemically, because it has been suggested that they are significant residues in ligand-linked kinase regulation. Measurements of the autoxidation rate, affinities, and kinetics of ligand binding revealed that all ...
Tópico(s): Erythrocyte Function and Pathophysiology
2006 - American Chemical Society | Biochemistry
Seiji Yamada, Hiro Nakamura, Eiji Kinoshita, Emiko Kinoshita‐Kikuta, Tohru Koike, Yoshitsugu Shiro,
Bacterial two-component systems (TCSs), which typically consist of a sensor histidine kinase (HK) and a response regulator (RR), have been investigated as attractive antibacterial drug targets. Unfortunately, current HK activity assays based on the quantification of autophosphorylated HKs are hampered by the instability of the phosphohistidine (pHis) product, rendering them ill-suited for high-throughput screenings. To address this challenge, we developed a simple HK activity assay using readily available ...
Tópico(s): RNA and protein synthesis mechanisms
2006 - Elsevier BV | Analytical Biochemistry
Kaori Kurashima-Ito, Yuichi Kasai, Kaito Hosono, Koji Tamura, Soichi Oue, Miho Isogai, Yutaka Ito, Hiro Nakamura, Yoshitsugu Shiro,
FixJ is a response regulator of the two-component signal transduction pathway involved in the transcriptional activation of nitrogen fixation genes of Sinorhizobium meliloti. Upon phosphorylation, FixJ transcriptionally activates the fixK and nifA promoters. We identified a FixJ recognition sequence of 16 bp in the high affinity binding site of the fixK promoter by means of a gel shift assay. In addition, the solution structure of the truncated C-terminal DNA binding domain of FixJ (FixJC) was solved ...
Tópico(s): Wastewater Treatment and Nitrogen Removal
2005 - American Chemical Society | Biochemistry
Hiro Nakamura, Hideyuki Kumita, Kiyohiro Imai, Tetsutarō Iizuka, Yoshitsugu Shiro,
The rhizobial FixL/FixJ system, a paradigm of heme-based oxygen sensors, belongs to the ubiquitous two-component signal transduction system. Oxygen-free (deoxy) FixL is autophosphorylated at an invariant histidine residue by using ATP and catalyzes the concomitant phosphoryl transfer to FixJ, but oxygen binding to the FixL heme moiety inactivates the kinase activity. Here we demonstrate that ADP acts as an allosteric effector, reducing the oxygen-binding affinity of the sensor domain in FixL when ...
Tópico(s): Vibrio bacteria research studies
2004 - National Academy of Sciences | Proceedings of the National Academy of Sciences
Takeshi Uchida, Tatsushi Mogi, Hiro Nakamura, Teizo Kitagawa,
To explore the role of a cross-link between side chains of Tyr-288 and His-284 at the heme-copper binuclear center, we prepared cytochrome bo where d4-Tyr, 1-[13C]Tyr, or 4-[13C]Tyr has been biosynthetically incorporated. Unexpectedly, the d4-Tyr-labeled enzyme showed a large decrease in the ubiquinol-1 oxidase and CO binding activities. Optical absorption and resonance Raman spectra identified the defect in the distal side of the heme-copper binuclear center. In the CO-bound d4-Tyr-labeled enzyme, ...
Tópico(s): Hemoglobin structure and function
2004 - Elsevier BV | Journal of Biological Chemistry
Hideyuki Kumita, Seiji Yamada, Hiro Nakamura, Yoshitsugu Shiro,
Tópico(s): Photosynthetic Processes and Mechanisms
2003 - Elsevier BV | Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Seiichi Taguchi, Hiro Nakamura, Tetsuya Hiraishi, Ichiro Yamato, Y. Doi,
In vitro evolution was applied to obtain highly active mutants of Ralstonia eutropha polyester synthase (PhbCRe), which is a key enzyme catalyzing the formation of polyhy-droxybutyrate (PHB) from (f?)-3-hydroxybutyryl-CoA (3HB-CoA). To search for beneficial mutations for activity improvement of this enzyme, we have conducted multi-step mutations, including activity loss and intragenic suppression-type activity reversion. Among 259 revertants, triple mutant E11S12 was obtained as the most active one ...
Tópico(s): Biofuel production and bioconversion
2002 - Oxford University Press | The Journal of Biochemistry
Hiroshi Endoh, Takaho Kaneko, Hiro Nakamura, Katsuhiko Doi, Eiji Takahashi,
An intracellular mechanism that senses decreases in tissue oxygen level and stimulates hypoxia-related gene expression has been reported in various cell types including the cardiac cell. The mechanism can also be activated by Co 2+ in normoxia. Thus we investigated the effects of prior chronic oral CoCl 2 on mechanical functions of isolated, perfused rat hearts in hypoxia-reoxygenation. In normoxic rats, 43 days of Co 2+ administration increased hematocrit from 45 ± 0.3% (control, n = 18) to 51 ± 0.6% ( ...
Tópico(s): High Altitude and Hypoxia
2000 - American Physical Society | AJP Heart and Circulatory Physiology
Hideyuki Miyatake, Masahiro Mukai, Sam‐Yong Park, Shin‐ichi Adachi, Koji Tamura, Hiro Nakamura, Kayako Nakamura, Terumasa Tsuchiya, Tetsutarō Iizuka, Yoshitsugu Shiro,
Tópico(s): Photosynthetic Processes and Mechanisms
2000 - Elsevier BV | Journal of Molecular Biology
Hideaki Shimizu, E. Obayashi, Yuki Gomi, Hiroshi Arakawa, Sam‐Yong Park, Hiro Nakamura, Shin‐ichi Adachi, Hirofumi Shoun, Yoshitsugu Shiro,
Fungal nitric-oxide reductase (NOR) is a heme enzyme that catalyzes the reduction of NO to N 2 O through its ferric-NO complex, the first intermediate of the catalysis. Crystal structures of the ferric-NO forms of wild type (WT) fungal NOR, and of the Ser 286 → Val and Ser 286 → Thr mutant enzymes were determined to 1.7-Å resolution at cryogenic temperature (100 K). This shows a slightly tilted and bent NO binding to the heme iron, in sharp contrast to the highly bent NO coordination found in ferrous hemoproteins. ...
Tópico(s): Photosynthetic Processes and Mechanisms
2000 - Elsevier BV | Journal of Biological Chemistry
Seed storage proteins of Japanese wheat (Triticum aestivum) varieties were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to identify the alleles for complex gene loci, Glu-A1, Glu-B1, and Glu-D1, which code for high molecular weight (HMW) subunits of glutenin in Japanese hexaploid wheat varieties. These were identified by comparison of subunit mobility with those previously found in hexaploid wheat. Twenty-four different, major glutenin HMW subunits were identified, and ...
Tópico(s): Phytase and its Applications
1999 - American Chemical Society | Journal of Agricultural and Food Chemistry
Yasuhiro Isogai, Motonori Ota, Tetsuro Fujisawa, Hiroyuki Izuno, Masahiro Mukai, Hiro Nakamura, Tetsutarō Iizuka, Ken Nishikawa,
We propose a simple method to find an amino acid sequence that is foldable into a globular protein with a desired structure based on a knowledge-based 3D−1D compatibility function. An asymmetric α-helical single-domain structure of sperm whale myoglobin consisting of 153 amino acid residues was chosen for the design target. The optimal sequence to fit the main-chain framework has been searched by recursive generation of the protein 3D profile. The heme-binding site was designed by fixing His64 and ...
Tópico(s): Porphyrin Metabolism and Disorders
1999 - American Chemical Society | Biochemistry