98 results on '"Ki-Seok Yoon"'
Search Results
2. Biochemical and structural characterization of a thermostable Dps protein with His‐type ferroxidase centers and outer metal‐binding sites
- Author
-
Takuo Minato, Takamasa Teramoto, Yoshimitsu Kakuta, Seiji Ogo, and Ki‐Seok Yoon
- Subjects
cyanobacteria ,DNA‐binding protein from starved cells ,His‐type ferroxidase center ,metal‐binding site ,thermostability ,Biology (General) ,QH301-705.5 - Abstract
The DNA‐binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from nonheterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O‐77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 demonstrated that it had higher thermostability than previously reported Dps proteins. X‐ray crystallographic analysis revealed that TlDps1 possessed His‐type ferroxidase centers within the cavity and unique metal‐binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability.
- Published
- 2020
- Full Text
- View/download PDF
3. Mechanistic investigation of the formation of H2 from HCOOH with a dinuclear Ru model complex for formate hydrogen lyase
- Author
-
Taisuke Tokunaga, Takeshi Yatabe, Takahiro Matsumoto, Tatsuya Ando, Ki-Seok Yoon, and Seiji Ogo
- Subjects
Mechanistic investigation ,H2 evolution ,formic acid ,formate hydrogen lyase model ,dinuclear Ru complex ,Materials of engineering and construction. Mechanics of materials ,TA401-492 ,Biotechnology ,TP248.13-248.65 - Abstract
We report the mechanistic investigation of catalytic H2 evolution from formic acid in water using a formate-bridged dinuclear Ru complex as a formate hydrogen lyase model. The mechanistic study is based on isotope-labeling experiments involving hydrogen isotope exchange reaction.
- Published
- 2017
- Full Text
- View/download PDF
4. Achieving a Carbon Neutral Future through Advanced Functional Materials and Technologies
- Author
-
Andrew Chapman, Elif Ertekin, Masanobu Kubota, Akihide Nagao, Kaila Bertsch, Arnaud Macadre, Toshihiro Tsuchiyama, Takuro Masamura, Setsuo Takaki, Ryosuke Komoda, Mohsen Dadfarnia, Brian Somerday, Alexander Tsekov Staykov, Joichi Sugimura, Yoshinori Sawae, Takehiro Morita, Hiroyoshi Tanaka, Kazuyuki Yagi, Vlad Niste, Prabakaran Saravanan, Shugo Onitsuka, Ki-Seok Yoon, Seiji Ogo, Toshinori Matsushima, Ganbaatar Tumen-Ulzii, Dino Klotz, Dinh Hoa Nguyen, George Harrington, Chihaya Adachi, Hiroshige Matsumoto, Leonard Kwati, Yukina Takahashi, Nuttavut Kosem, Tatsumi Ishihara, Miho Yamauchi, Bidyut Baran Saha, Md. Amirul Islam, Jin Miyawaki, Harish Sivasankaran, Masamichi Kohno, Shigenori Fujikawa, Roman Selyanchyn, Takeshi Tsuji, Yukihiro Higashi, Reiner Kirchheim, and Petros Sofronis
- Subjects
General Chemistry - Published
- 2022
5. C–H Arylation of Benzene with Aryl Halides using H2and a Water‐Soluble Rh‐Based Electron Storage Catalyst
- Author
-
Yukina Takahashi, Hidetaka Nakai, Ki-Seok Yoon, Seiji Ogo, Tamon Tome, Takahiro Matsumoto, and Takeshi Yatabe
- Subjects
Aqueous solution ,Chemistry ,Aryl ,Organic Chemistry ,Inorganic chemistry ,Halide ,General Chemistry ,Electron source ,Catalysis ,Electron storage ,chemistry.chemical_compound ,Water soluble ,Benzene - Abstract
This paper reports the first example of C-H arylation of benzene under mild conditions, using H2 as an electron source {turnover numbers (TONs)=0.7-2.0 for 24 h}. The reaction depends on a Rh-based electron storage catalyst, and proceeds at room temperature and in aqueous solution. Furthermore, the H2 is inactive during the radical transfer step, greatly reducing unwanted side reactions.
- Published
- 2021
6. Reductive C(sp3)–C(sp3) homo-coupling of benzyl or allyl halides with H2 using a water-soluble electron storage catalyst
- Author
-
Takeshi Yatabe, Sayaka Futakuchi, Keishi Miyazawa, Daiki Shimauchi, Yukina Takahashi, Ki-Seok Yoon, Hidetaka Nakai, and Seiji Ogo
- Subjects
General Chemical Engineering ,General Chemistry - Abstract
Four requirements for the reductive C(sp3)–C(sp3) homo-coupling of benzyl/allyl halides in aqueous solution by using H2 as an electron source are described.
- Published
- 2021
7. Biochemical and structural characterization of a thermostable Dps protein with His‐type ferroxidase centers and outer metal‐binding sites
- Author
-
Ki Seok Yoon, Seiji Ogo, Takamasa Teramoto, Takuo Minato, and Yoshimitsu Kakuta
- Subjects
Models, Molecular ,0301 basic medicine ,Cyanobacteria ,Protein Conformation ,Microorganism ,DNA-binding protein from starved cells ,Metal Binding Site ,Crystallography, X-Ray ,cyanobacteria ,DNA-binding protein ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Bacterial Proteins ,Histidine ,lcsh:QH301-705.5 ,Research Articles ,Thermostability ,Binding Sites ,biology ,Chemistry ,Thermophile ,Temperature ,Ceruloplasmin ,DNA‐binding protein from starved cells ,biology.organism_classification ,thermostability ,Trace Elements ,DNA-Binding Proteins ,030104 developmental biology ,metal‐binding site ,lcsh:Biology (General) ,Biochemistry ,His‐type ferroxidase center ,030220 oncology & carcinogenesis ,biology.protein ,Research Article - Abstract
The DNA‐binding protein from starved cells (Dps) is found in a wide range of microorganisms, and it has been well characterized. However, little is known about Dps proteins from nonheterocystous filamentous cyanobacteria. In this study, a Dps protein from the thermophilic nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O‐77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 demonstrated that it had higher thermostability than previously reported Dps proteins. X‐ray crystallographic analysis revealed that TlDps1 possessed His‐type ferroxidase centers within the cavity and unique metal‐binding sites located on the surface of the protein, which presumably contributed to its exceedingly high thermostability., A DNA‐binding protein from starved cells (Dps) protein from nonheterocystous filamentous cyanobacterium Thermoleptolyngbya sp. O‐77 (TlDps1) was purified and characterized. PAGE and CD analyses of TlDps1 illustrated that it had higher thermostability than previously reported Dps proteins. X‐ray crystallographic analysis revealed that TlDps1 possessed His‐type ferroxidase centers within the cavity and unique metal‐binding sites located on the surface of the protein.
- Published
- 2020
8. A NiRhS fuel cell catalyst – lessons from hydrogenase
- Author
-
Kenji Kaneko, Ki Seok Yoon, Takeshi Yatabe, Takashi Hibino, Tatsuya Ando, Yuki Mori, Yukio Sato, Seiji Ogo, Takahiro Matsumoto, and Le Tu Thi Minh
- Subjects
Materials science ,Hydrogenase ,chemistry.chemical_element ,Heterogeneous catalysis ,Catalysis ,Rhodium ,law.invention ,Electric Power Supplies ,Biomimetics ,Coordination Complexes ,Nickel ,law ,Materials Chemistry ,Electrodes ,Metals and Alloys ,General Chemistry ,Cathode ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Anode ,Chemical engineering ,chemistry ,Ceramics and Composites ,2,6-Dichloroindophenol ,Platinum ,Oxidation-Reduction ,Sulfur - Abstract
We present a novel fuel cell heterogeneous catalyst based on rhodium, nickel and sulfur with power densities 5–28% that of platinum. The NiRhS heterogeneous catalyst was developed via a homogeneous model complex of the [NiFe]hydrogenases (H2ases) and can act as both the cathode and anode of a fuel cell.
- Published
- 2020
9. Reductive C(sp
- Author
-
Takeshi, Yatabe, Sayaka, Futakuchi, Keishi, Miyazawa, Daiki, Shimauchi, Yukina, Takahashi, Ki-Seok, Yoon, Hidetaka, Nakai, and Seiji, Ogo
- Abstract
This paper reports the first example of a reductive C(sp
- Published
- 2021
10. Non-conventional octameric structure of C-phycocyanin
- Author
-
Toshio Moriya, Masato Akutsu, Ki Seok Yoon, Yoshimitsu Kakuta, Kaho Yamada, Takamasa Teramoto, Masato Kawasaki, Takuo Minato, Nguyen Khac Hung, Naruhiko Adachi, Toshiya Senda, and Seiji Ogo
- Subjects
Cyanobacteria ,biology ,QH301-705.5 ,Chemistry ,Thermophile ,Phycocyanin ,Medicine (miscellaneous) ,C-Phycocyanin ,Random hexamer ,biology.organism_classification ,Article ,General Biochemistry, Genetics and Molecular Biology ,Crystal ,Crystallography ,Bacterial Proteins ,Cryoelectron microscopy ,Phycobilisome ,Histone octamer ,Biology (General) ,General Agricultural and Biological Sciences ,X-ray crystallography ,Photosystem - Abstract
C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to photosystems I and II. X-ray crystallographic and electron microscopy (EM) analyses have revealed the structure of CPC to be a closed toroidal hexamer by assembling two trimers. In this study, the structural characterization of non-conventional octameric CPC is reported for the first time. Analyses of the crystal and cryogenic EM structures of the native CPC from filamentous thermophilic cyanobacterium Thermoleptolyngbya sp. O–77 unexpectedly illustrated the coexistence of conventional hexamer and novel octamer. In addition, an unusual dimeric state, observed via analytical ultracentrifugation, was postulated to be a key intermediate structure in the assemble of the previously unobserved octamer. These observations provide new insights into the assembly processes of CPCs and the mechanism of energy transfer in the light-harvesting complexes., Takuo Minato and colleagues determine the crystal and cryo-EM structures of the native C-phycocyanin (CPC) from the thermophilic cyanobacterium, Thermoleptolyngbya sp. O77, which was found to adopt both a conventional hexameric structure and a novel octameric assembly. These findings provide new insights into the assembly of CPCs and their mechanism of energy transfer.
- Published
- 2021
11. Synthesis of acetic acid from CO2, CH3I and H2 using a water-soluble electron storage catalyst
- Author
-
Kazuki Kamitakahara, Takahiro Matsumoto, Ki Seok Yoon, Seiji Ogo, Tatsuya Ando, Takeshi Yatabe, Takao Enomoto, and Kaede Higashijima
- Subjects
Ligand ,Metals and Alloys ,General Chemistry ,Crystal structure ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Metal ,Solvent ,Electron storage ,Acetic acid ,chemistry.chemical_compound ,chemistry ,visual_art ,Polymer chemistry ,Materials Chemistry ,Ceramics and Composites ,visual_art.visual_art_medium ,Lewis acids and bases - Abstract
This paper reports a possible mechanism of acetic acid formation from CO2, CH3I and H2 in aqueous media and the central role played by a water-soluble Rh-based electron storage catalyst. In addition to water-solubility, we also report the crystal structures of two presumed intermediates. These findings together reveal (1) the advantage of water, not only as a green solvent, but also as a reactive Lewis base to extract H+ from H2, (2) the role of the metal (Rh) centre as a point for storing electrons from H2 and (3) the importance of an electron-withdrawing ligand (quaterpyridine, qpy) that supports electron storage.
- Published
- 2021
12. C-H Arylation of Benzene with Aryl Halides using H
- Author
-
Takeshi, Yatabe, Tamon, Tome, Yukina, Takahashi, Takahiro, Matsumoto, Ki-Seok, Yoon, Hidetaka, Nakai, and Seiji, Ogo
- Abstract
This paper reports the first example of C-H arylation of benzene under mild conditions, using H
- Published
- 2021
13. Synthesis of acetic acid from CO
- Author
-
Takeshi, Yatabe, Kazuki, Kamitakahara, Kaede, Higashijima, Tatsuya, Ando, Takahiro, Matsumoto, Ki-Seok, Yoon, Takao, Enomoto, and Seiji, Ogo
- Abstract
This paper reports a possible mechanism of acetic acid formation from CO2, CH3I and H2 in aqueous media and the central role played by a water-soluble Rh-based electron storage catalyst. In addition to water-solubility, we also report the crystal structures of two presumed intermediates. These findings together reveal (1) the advantage of water, not only as a green solvent, but also as a reactive Lewis base to extract H+ from H2, (2) the role of the metal (Rh) centre as a point for storing electrons from H2 and (3) the importance of an electron-withdrawing ligand (quaterpyridine, qpy) that supports electron storage.
- Published
- 2021
14. Cp*Ir complex with mesobiliverdin ligand isolated from Thermoleptolyngbya sp. O-77
- Author
-
Kaho Yamada, Takeshi Yatabe, Ki-Seok Yoon, and Seiji Ogo
- Subjects
Inorganic Chemistry ,Organic Chemistry ,Materials Chemistry ,Physical and Theoretical Chemistry ,Biochemistry - Published
- 2022
15. [NiFe], [FeFe], and [Fe] hydrogenase models from isomers
- Author
-
Ki Seok Yoon, Keishi Miyazawa, Seiji Ogo, Takeshi Yatabe, Mitsuhiro Kikkawa, Miho Isegawa, Takahiro Matsumoto, Tatsuya Ando, Ryunosuke Yamasaki, Takahiro Kishima, and Shinya Hayami
- Subjects
chemistry.chemical_classification ,Chemical Physics ,Multidisciplinary ,Hydrogenase ,010405 organic chemistry ,Infrared ,Ligand ,fungi ,food and beverages ,SciAdv r-articles ,010402 general chemistry ,Electrochemistry ,01 natural sciences ,0104 chemical sciences ,Catalysis ,Chemistry ,Crystallography ,Enzyme ,chemistry ,Mössbauer spectroscopy ,Molecule ,Research Articles ,Research Article - Abstract
Three isomers of the same NiFe complex can mimic the catalytic properties of [NiFe], [FeFe], and [Fe] hydrogenase enzymes., The study of hydrogenase enzymes (H2ases) is necessary because of their importance to a future hydrogen energy economy. These enzymes come in three distinct classes: [NiFe] H2ases, which have a propensity toward H2 oxidation; [FeFe] H2ases, which have a propensity toward H2 evolution; and [Fe] H2ases, which catalyze H− transfer. Modeling these enzymes has so far treated them as different species, which is understandable given the different cores and ligand sets of the natural molecules. Here, we demonstrate, using x-ray analysis and nuclear magnetic resonance, infrared, Mössbauer spectroscopies, and electrochemical measurement, that the catalytic properties of all three enzymes can be mimicked with only three isomers of the same NiFe complex.
- Published
- 2020
16. Multifunctional Catalysts for H 2 O 2 ‐Resistant Hydrogen Fuel Cells
- Author
-
Takeshi Yatabe, Tatsuya Ando, Yuki Mori, Takahiro Matsumoto, Ki Seok Yoon, Seiji Ogo, and Mitsuhiro Kikkawa
- Subjects
Materials science ,010405 organic chemistry ,General Medicine ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Catalysis ,Cathode ,0104 chemical sciences ,Cathode catalyst ,law.invention ,Rendering (animal products) ,Chemical engineering ,law ,Hydrogen fuel ,Fuel cells - Abstract
The development of hydrogen fuel cells is greatly hindered by the unwanted generation of H2 O2 at the cathode. A non-Pt cathode catalyst is now shown to be capable of simultaneously reducing both O2 and H2 O2 , thus rendering H2 O2 a useful part of the feed stream. The applicability of this unique catalyst is demonstrated by employing it in a fuel cell running on H2 /CO and O2 /H2 O2 .
- Published
- 2018
17. Oxidation of Guanosine Monophosphate with O2 via a Ru-peroxo Complex in Water
- Author
-
Mitsuhiro Kikkawa, Makoto Takenaka, Tatsuya Ando, Ki Seok Yoon, Takahiro Matsumoto, Seiji Ogo, and Takeshi Yatabe
- Subjects
chemistry.chemical_classification ,Reactive oxygen species ,010405 organic chemistry ,DNA damage ,Organic Chemistry ,chemistry.chemical_element ,RNA ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Oxygen ,0104 chemical sciences ,Ruthenium ,Metal ,chemistry.chemical_compound ,chemistry ,visual_art ,Guanosine monophosphate ,visual_art.visual_art_medium ,DNA - Abstract
Oxidative damage of DNA by reactive oxygen species (ROS) is responsible for aging and cancer. Although many studies of DNA damage by ROS have been conducted, there have been no reports of the oxidation of RNA components, such as guanosine monophosphate, by metal-based species in water. Here, we report the first case of oxidation of guanosine monophosphate to 8-oxoguanosine monophosphate by a metal-based oxygen bound species, derived from O2 and in water.
- Published
- 2018
18. Redox-dependent conformational changes of a proximal [4Fe–4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2
- Author
-
Koji Nishikawa, Kubota Shintaro, J. Kim, Masaru Tateno, Ki Seok Yoon, Yoshiki Higuchi, Hulin Tai, Jiyoung Kang, Seiji Ogo, H. Matsuura, Shun Hirota, Noor Dina Muhd Noor, and Yasuhito Shomura
- Subjects
0301 basic medicine ,chemistry.chemical_classification ,biology ,Stereochemistry ,Chemistry ,Metals and Alloys ,Active site ,General Chemistry ,Redox ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,03 medical and health sciences ,030104 developmental biology ,Oxidoreductase ,Materials Chemistry ,Ceramics and Composites ,biology.protein ,Cluster (physics) ,Molecule ,NiFe hydrogenase ,Citrobacter sp - Abstract
Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe–4S] cluster proximal to the Ni–Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe–4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.
- Published
- 2018
19. Mechanistic investigation of the formation of H2 from HCOOH with a dinuclear Ru model complex for formate hydrogen lyase
- Author
-
Takahiro Matsumoto, Taisuke Tokunaga, Seiji Ogo, Ki Seok Yoon, Takeshi Yatabe, and Tatsuya Ando
- Subjects
30 Bio-inspired and biomedical materials ,Focus on Carbon-neutral Energy Science and Technology ,Hydrogen ,formic acid ,Formic acid ,lcsh:Biotechnology ,106 Metallic materials ,chemistry.chemical_element ,dinuclear Ru complex ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Article ,Catalysis ,chemistry.chemical_compound ,lcsh:TP248.13-248.65 ,lcsh:TA401-492 ,General Materials Science ,Formate ,010405 organic chemistry ,Chemistry ,Hydrogen isotope ,Lyase ,formate hydrogen lyase model ,0104 chemical sciences ,lcsh:Materials of engineering and construction. Mechanics of materials ,H2 evolution ,Mechanistic investigation - Abstract
We report the mechanistic investigation of catalytic H2 evolution from formic acid in water using a formate-bridged dinuclear Ru complex as a formate hydrogen lyase model. The mechanistic study is based on isotope-labeling experiments involving hydrogen isotope exchange reaction., Graphical Abstract
- Published
- 2017
20. Mechanistic Insight into Switching between H2- or O2-Activation by Simple Ligand Effects of [NiFe]hydrogenase Models
- Author
-
Ki Seok Yoon, Takahiro Kishima, Seiji Ogo, Takeshi Yatabe, and Takahiro Matsumoto
- Subjects
Hydrogenase ,010405 organic chemistry ,Chemistry ,Hydride ,Ligand ,Organic Chemistry ,010402 general chemistry ,Cleavage (embryo) ,Photochemistry ,01 natural sciences ,Heterolysis ,0104 chemical sciences ,Inorganic Chemistry ,Physical and Theoretical Chemistry ,NiFe hydrogenase ,Saturation (chemistry) - Abstract
We present a mechanistic investigation for the activation of H2 and O2, induced by a simple ligand effect within [NiFe] models for O2-tolerant [NiFe]hydrogenase. Kinetic study reveals Michaelis–Menten type saturation behaviors for both H2 and O2 activation, which is the same behavior as that found in O2-tolerant [NiFe]hydrogenase. Such saturation behavior is caused by H2 complexation followed by heterolytic cleavage of H2 by an outer-sphere base, resulting in the formation of a hydride species showing hydridic character.
- Published
- 2017
21. A Fusion of Biomimetic Fuel and Solar Cells Based on Hydrogenase, Photosystem II, and Cytochrome c Oxidase
- Author
-
Takao Enomoto, Takahiro Matsumoto, Suzuki Kazuharu, Takeshi Yatabe, Seiji Ogo, Mitsuhiro Kikkawa, Kenji Kaneko, and Ki Seok Yoon
- Subjects
Oxidase test ,Fusion ,Hydrogenase ,biology ,Photosystem II ,Organic Chemistry ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Photochemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Inorganic Chemistry ,chemistry ,biology.protein ,Cytochrome c oxidase ,Iridium ,Physical and Theoretical Chemistry ,0210 nano-technology ,Platinum - Abstract
We report an Ir complex as an anode catalyst capable of switching between a hydrogenase-type fuel-cell mode and a photosystem II-type solar-cell mode. This catalyst is connected to carbon-black-supported platinum as a cathode catalyst, which reduces dioxygen in a manner analogous to cytochrome c oxidase. Together, they make a system capable of switching between the two modes.
- Published
- 2017
22. Structural basis of the redox switches in the NAD + -reducing soluble [NiFe]-hydrogenase
- Author
-
Y. Ikeda, Hulin Tai, H. Nakagawa, Shun Hirota, Yasuo Igarashi, Hirofumi Nishihara, Masaharu Ishii, Ki Seok Yoon, Yoshiki Higuchi, H. Nakashima, Midori Taketa, Yasuhito Shomura, and Seiji Ogo
- Subjects
0301 basic medicine ,chemistry.chemical_classification ,Multidisciplinary ,Hydrogenase ,biology ,Chemistry ,Stereochemistry ,Active site ,Flavin mononucleotide ,Electron acceptor ,Nicotinamide adenine dinucleotide ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Redox ,Cofactor ,0104 chemical sciences ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,biology.protein ,NAD+ kinase - Abstract
How a hydrogenase protects its active site Hydrogen-metabolizing organisms use an [NiFe]-hydrogenase to catalyze hydrogen oxidation. One type of [NiFe]-hydrogenase, the NAD + -reducing soluble [NiFe]-hydrogenase (SH), couples reduction of NAD + to the oxidation of hydrogen. Shomura et al. solved the structure of SH from an H 2 -oxidizing bacterium in both the air-oxidized and the active reduced state. In the reduced state, the NiFe catalytic center in SH has the same ligand coordination as in other [NiFe]-hydrogenases. However, the air-oxidized active site has an unusual coordination geometry that would prevent O 2 from accessing the site and so may protect against irreversible oxidation. Science , this issue p. 928
- Published
- 2017
23. Acetyl-CoA production by encapsulated pyruvate ferredoxin oxidoreductase in alginate hydrogels
- Author
-
Makoto Takenaka, Ki Seok Yoon, Takahiro Matsumoto, and Seiji Ogo
- Subjects
0301 basic medicine ,Environmental Engineering ,Alginates ,Pyruvate Synthase ,Pyruvate-Ferredoxin Oxidoreductase ,Bioengineering ,02 engineering and technology ,Catalysis ,law.invention ,03 medical and health sciences ,chemistry.chemical_compound ,Citrobacter ,Glucuronic Acid ,Magazine ,Acetyl Coenzyme A ,law ,Operational stability ,Waste Management and Disposal ,chemistry.chemical_classification ,Renewable Energy, Sustainability and the Environment ,Hexuronic Acids ,Acetyl-CoA ,Hydrogels ,General Medicine ,021001 nanoscience & nanotechnology ,030104 developmental biology ,Enzyme ,chemistry ,Biochemistry ,Self-healing hydrogels ,Alginate hydrogel ,0210 nano-technology - Abstract
Pyruvate ferredoxin oxidoreductase from Citrobacter sp. S-77 (PFORS77) was purified in order to develop a method for acetyl-CoA production. Although the purified PFORS77 showed high O2-sensitivity, the activity could be remarkably stabilized in anaerobic conditions. PFORS77 was effectively immobilized on ceramic hydroxyapatite (PFORS77-HA) with an efficiency of more than 96%, however, after encapsulation of PFORS77-HA in alginate, the rate of catalytic acetyl-CoA production was highly reduced to 36% when compared to that of the free enzyme. However, the operational stability of the PFORS77-HA in alginate hydrogels was remarkable, retaining over 68% initial activity even after ten repeated cycles. The results suggested that the PFORS77-HA hydrogels have a high potential for biotechnological application.
- Published
- 2017
24. Nitrogen Fixation Genes and Nitrogenase Activity of the Non-Heterocystous Cyanobacterium Thermoleptolyngbya sp. O-77
- Author
-
Kohsei Tsuji, Ki Seok Yoon, Kien Trung Tran, Seiji Ogo, and Nga T. Nguyen
- Subjects
0301 basic medicine ,Cyanobacteria ,Strain (chemistry) ,biology ,Chemistry ,Thermophile ,Soil Science ,Nitrogenase ,Plant Science ,General Medicine ,biology.organism_classification ,03 medical and health sciences ,030104 developmental biology ,Botany ,Nitrogen fixation ,Peptide sequence ,Nitrogen cycle ,Gene ,Ecology, Evolution, Behavior and Systematics - Abstract
Cyanobacteria are widely distributed in marine, aquatic, and terrestrial ecosystems, and play an important role in the global nitrogen cycle. In the present study, we examined the genome sequence of the thermophilic non-heterocystous N2-fixing cyanobacterium, Thermoleptolyngbya sp. O-77 (formerly known as Leptolyngbya sp. O-77) and characterized its nitrogenase activity. The genome of this cyanobacterial strain O-77 consists of a single chromosome containing a nitrogen fixation gene cluster. A phylogenetic analysis indicated that the NifH amino acid sequence from strain O-77 was clustered with those from a group of mesophilic species: the highest identity was found in Leptolyngbya sp. KIOST-1 (97.9% sequence identity). The nitrogenase activity of O-77 cells was dependent on illumination, whereas a high intensity of light of 40 μmol m-2 s-1 suppressed the effects of illumination.
- Published
- 2017
25. A MnI Model for the Photoinhibited Species of Oxygen-evolving Complex
- Author
-
Mitsuhiro Kikkawa, Taisuke Tokunaga, Seiji Ogo, Takeshi Yatabe, Takahiro Matsumoto, and Ki Seok Yoon
- Subjects
Absorption spectroscopy ,010405 organic chemistry ,Chemistry ,Infrared spectroscopy ,General Chemistry ,ESI mass spectrometry ,Oxygen-evolving complex ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Polymer chemistry ,Cyclam ,Reactivity (chemistry) - Abstract
We report the reactivity of a new MnI(cyclam) complex (cyclam: 1,4,8,11-tetraazacyclotetradecane) toward O2 and H2O as a model for the photoinhibited species of oxygen-evolving complex (OEC). The reactivity varies according to the number of CO ligands. A MnI dicarbonyl complex, [MnI(cyclam)(CO)2]+ reacts with O2, but not with H2O, to form a bis(μ-oxo)Mn2III,IV complex, though a MnI tricarbonyl complex, [MnI(cyclam)(CO)3]+ does not react with either O2 or H2O. Newly synthesized MnI(cyclam) dicarbonyl complex was characterized by ESI mass spectrometry, UV–vis absorption spectroscopy, IR spectroscopy, and X-ray analysis.
- Published
- 2018
26. Improved purification, crystallization and crystallographic study of Hyd-2-type [NiFe]-hydrogenase fromCitrobactersp. S-77
- Author
-
Hirofumi Nishihara, Noor Dina Muhd Noor, Seiji Ogo, Ki Seok Yoon, Yoshiki Higuchi, and Koji Nishikawa
- Subjects
0301 basic medicine ,Resolution (mass spectrometry) ,Biophysics ,Polyethylene glycol ,Crystallography, X-Ray ,Biochemistry ,Chromatography, Affinity ,Research Communications ,law.invention ,Catalysis ,Crystal ,03 medical and health sciences ,chemistry.chemical_compound ,Citrobacter ,Bacterial Proteins ,Hydrogenase ,Structural Biology ,law ,Genetics ,medicine ,Crystallization ,Citrobacter sp ,Chromatography ,Chemistry ,Condensed Matter Physics ,Trypsin ,Oxygen ,Kinetics ,Crystallography ,030104 developmental biology ,NiFe hydrogenase ,Hydrogen ,medicine.drug - Abstract
The purification procedure of Hyd-2-type [NiFe]-hydrogenase fromCitrobactersp. S-77 was improved by applying treatment with trypsin before chromatography. Purified protein samples both with and without trypsin treatment were successfully crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol as a precipitant. Both crystals belonged to space groupP21, with unit-cell parametersa= 63.90,b= 118.89,c= 96.70 Å, β = 100.61° for the protein subjected to trypsin treatment anda= 65.38,b= 121.45,c= 98.63 Å, β = 102.29° for the sample not treated with trypsin. The crystal obtained from the trypsin-treated protein diffracted to 1.60 Å resolution, which is considerably better than the 2.00 Å resolution obtained without trypsin treatment. The [NiFe]-hydrogenase fromCitrobactersp. S-77 retained catalytic activity with some amount of O2, indicating that it has clear O2tolerance.
- Published
- 2016
27. Structure and Reactivity of a Ru-based Peroxide Complex as a Reactive Intermediate of O2-Promoted Activation of a C–H Bond in a Cp* Ligand
- Author
-
Takahiro Kishima, Hideaki Nagano, Ki Seok Yoon, Takahiro Matsumoto, Seiji Ogo, Takeshi Yatabe, and Mikio Yamasaki
- Subjects
C h bond ,010405 organic chemistry ,Chemistry ,Ligand ,Reactive intermediate ,Nanotechnology ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Peroxide ,Medicinal chemistry ,0104 chemical sciences ,chemistry.chemical_compound ,Reactivity (chemistry) - Abstract
We report the first example of the characterization of a Ru-based peroxide intermediate of O2-promoted activation of a C–H bond of the pentamethylcyclopentadienyl (Cp*) ligand. The peroxide complex activates the C–H bond to form a tetramethylfulvene complex. We propose a proton-coupled electron-transfer (PCET) mechanism of the C–H bond activation based on the structures and properties of the peroxide and tetramethylfulvene complexes.
- Published
- 2017
28. Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O
- Author
-
Noor Dina Muhd, Noor, Hiroaki, Matsuura, Koji, Nishikawa, Hulin, Tai, Shun, Hirota, Jaehyun, Kim, Jiyoung, Kang, Masaru, Tateno, Ki-Seok, Yoon, Seiji, Ogo, Shintaro, Kubota, Yasuhito, Shomura, and Yoshiki, Higuchi
- Subjects
Iron-Sulfur Proteins ,Models, Molecular ,Oxygen ,Hydrogenase ,Protein Conformation ,Catalytic Domain ,Spectroscopy, Fourier Transform Infrared ,Electron Spin Resonance Spectroscopy ,Hydrogen Bonding ,Oxidation-Reduction - Abstract
Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.
- Published
- 2018
29. Multifunctional Catalysts for H
- Author
-
Yuki, Mori, Tatsuya, Ando, Takahiro, Matsumoto, Takeshi, Yatabe, Mitsuhiro, Kikkawa, Ki-Seok, Yoon, and Seiji, Ogo
- Abstract
The development of hydrogen fuel cells is greatly hindered by the unwanted generation of H
- Published
- 2018
30. Oxidation of Guanosine Monophosphate with O
- Author
-
Makoto, Takenaka, Mitsuhiro, Kikkawa, Takahiro, Matsumoto, Takeshi, Yatabe, Tatsuya, Ando, Ki-Seok, Yoon, and Seiji, Ogo
- Abstract
Oxidative damage of DNA by reactive oxygen species (ROS) is responsible for aging and cancer. Although many studies of DNA damage by ROS have been conducted, there have been no reports of the oxidation of RNA components, such as guanosine monophosphate, by metal-based species in water. Here, we report the first case of oxidation of guanosine monophosphate to 8-oxoguanosine monophosphate by a metal-based oxygen bound species, derived from O
- Published
- 2018
31. Glyceraldehyde-3-phosphate dehydrogenase from
- Author
-
Seiji Ogo, Ki Seok Yoon, and Kohsei Tsuji
- Subjects
0301 basic medicine ,glyceraldehyde‐3‐phosphate dehydrogenase ,Coenzyme A ,post‐translational modification ,Dehydrogenase ,General Biochemistry, Genetics and Molecular Biology ,Dithiothreitol ,redox regulation ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Citrobacter ,stomatognathic system ,Glyceraldehyde 3-phosphate dehydrogenase ,Research Articles ,chemistry.chemical_classification ,biology ,S‐thiolation ,Glyceraldehyde-3-Phosphate Dehydrogenases ,Glutathione ,Enzyme assay ,Oxidative Stress ,030104 developmental biology ,Enzyme ,chemistry ,Biochemistry ,030220 oncology & carcinogenesis ,biology.protein ,Protein Processing, Post-Translational ,Cysteine ,Research Article - Abstract
Protein CoAlation (S-thiolation by coenzyme A) has recently emerged as an alternative redox-regulated post-translational modification by which protein thiols are covalently modified with coenzyme A (CoA). However, little is known about the role and mechanism of this post-translational modification. In the present study, we investigated CoAlation of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from a facultative anaerobic Gram-negative bacterium Citrobacter sp. S-77 (Cb GAPDH). GAPDH is a key glycolytic enzyme whose activity relies on the thiol-based redox-regulated post-translational modifications of active-site cysteine. LC-MS/MS analysis revealed that CoAlation of Cb GAPDH occurred in vivo under sodium hypochlorite (NaOCl) stress. The purified Cb GAPDH was highly sensitive to overoxidation by H2O2 and NaOCl, which resulted in irreversible enzyme inactivation. By contrast, treatment with coenzyme A disulphide (CoASSCoA) or H2O2/NaOCl in the presence of CoA led to CoAlation and inactivation of the enzyme; activity could be recovered after incubation with dithiothreitol, glutathione and CoA. CoAlation of the enzyme in vitro was confirmed by mass spectrometry. The presence of a substrate, glyceraldehyde-3-phosphate, fully protected Cb GAPDH from inactivation by CoAlation, suggesting that the inactivation is due to the formation of mixed disulphides between CoA and the active-site cysteine Cys149. A molecular docking study also supported the formation of mixed disulphide without steric constraints. These observations suggest that CoAlation is an alternative mechanism to protect the redox-sensitive thiol (Cys149) of Cb GAPDH against irreversible oxidation, thereby regulating enzyme activity under oxidative stress.
- Published
- 2018
32. Structural differences of oxidized iron–sulfur and nickel–iron cofactors in O2-tolerant and O2-sensitive hydrogenases studied by X-ray absorption spectroscopy
- Author
-
Oliver Lenz, Hirofumi Nishihara, Petko Chernev, Fraser A. Armstrong, Nils Leidel, Kajsa G.V. Sigfridsson, Marc Rousset, Antonio L. De Lacey, Ki Seok Yoon, Oliver Sanganas, Michael Haumann, Sébastien Dementin, Alison Parkin, Lund University [Lund], Humboldt-Universität zu Berlin, Freie Universität Berlin, Konkuk University, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Tokyo Institute of Technology [Tokyo] (TITECH), Department of Chemistry [York, UK], University of York [York, UK], Inorganic Chemistry Laboratory [Oxford], University of Oxford [Oxford], Bioénergétique et Ingénierie des Protéines (BIP ), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), German Research Foundation, Röntgen-Ångström Cluster, Ministerio de Economía y Competitividad (España), Royal Society (UK), Humboldt University Of Berlin, Konkuk University [Seoul], University of Oxford, and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Iron-Sulfur Proteins ,Absorption spectroscopy ,[SDV]Life Sciences [q-bio] ,Inorganic chemistry ,O2-tolerance ,Biophysics ,chemistry.chemical_element ,010402 general chemistry ,FeS cluster ,01 natural sciences ,Oxygen ,Biochemistry ,[NiFe]-hydrogenase ,03 medical and health sciences ,Electron transfer ,chemistry.chemical_compound ,Hydrogenase ,030304 developmental biology ,0303 health sciences ,X-ray absorption spectroscopy ,Binding Sites ,biology ,Chemistry ,[NiFe] active site ,Active site ,Cell Biology ,0104 chemical sciences ,3. Good health ,Bond length ,Nickel ,Cubane ,biology.protein ,Oxidation-Reduction - Abstract
The class of [NiFe]-hydrogenases comprises oxygen-sensitive periplasmic (PH) and oxygen-tolerant membrane-bound (MBH) enzymes. For three PHs and four MBHs from six bacterial species, structural features of the nickel–iron active site of hydrogen turnover and of the iron–sulfur clusters functioning in electron transfer were determined using X-ray absorption spectroscopy (XAS). Fe-XAS indicated surplus oxidized iron and a lower number of ~ 2.7 Å Fe–Fe distances plus additional shorter and longer distances in the oxidized MBHs compared to the oxidized PHs. This supported a double-oxidized and modified proximal FeS cluster in all MBHs with an apparent trimer-plus-monomer arrangement of its four iron atoms, in agreement with crystal data showing a [4Fe3S] cluster instead of a [4Fe4S] cubane as in the PHs. Ni-XAS indicated coordination of the nickel by the thiol group sulfurs of four conserved cysteines and at least one iron–oxygen bond in both MBH and PH proteins. Structural differences of the oxidized inactive [NiFe] cofactor of MBHs in the Ni-B state compared to PHs in the Ni–A state included a ~ 0.05 Å longer Ni-O bond, a two times larger spread of the Ni–S bond lengths, and a ~ 0.1 Å shorter Ni–Fe distance. The modified proximal [4Fe3S] cluster, weaker binding of the Ni–Fe bridging oxygen species, and an altered localization of reduced oxygen species at the active site may each contribute to O2 tolerance., M.H. thanks the Deutsche Forschungsgemeinschaft (DFG) for a Heisenberg Fellowship and the DFG (grants Ha3265/3-1 and Ha3265/6-1) and the Bundesministerium für Bildung und Wissenschaft (grant 05K14KE1 within the Röntgen-Angström Cluster) for the financial support. A.L.D.L thanks MINECO (project CTQ2012-32448) for the financial support. F.A.A. is a Royal Society Wolfson Research Merit Award holder.
- Published
- 2015
- Full Text
- View/download PDF
33. [NiFe]Hydrogenase fromCitrobactersp. S-77 Surpasses Platinum as an Electrode for H2Oxidation Reaction
- Author
-
Takahiro Matsumoto, Shigenobu Eguchi, Hidetaka Nakai, Takashi Hibino, Ki-Seok Yoon, and Seiji Ogo
- Subjects
General Medicine - Published
- 2014
34. [NiFe]Hydrogenase fromCitrobactersp. S-77 Surpasses Platinum as an Electrode for H2Oxidation Reaction
- Author
-
Takashi Hibino, Shigenobu Eguchi, Hidetaka Nakai, Takahiro Matsumoto, Ki Seok Yoon, and Seiji Ogo
- Subjects
Hydrogenase ,Hydrogen ,Bioelectric Energy Sources ,Chemistry ,Inorganic chemistry ,chemistry.chemical_element ,General Chemistry ,Redox ,Catalysis ,Cathode ,Anode ,law.invention ,chemistry.chemical_compound ,Citrobacter ,law ,Dielectric Spectroscopy ,Electrode ,Platinum ,Electrodes ,Oxidation-Reduction ,Carbon monoxide - Abstract
Reported herein is an electrode for dihydrogen (H2) oxidation, and it is based on [NiFe]Hydrogenase from Citrobacter sp. S-77 ([NiFe]S77). It has a 637 times higher mass activity than Pt (calculated based on 1 mg of [NiFe]S77 or Pt) at 50 mV in a hydrogen half-cell. The [NiFe]S77 electrode is also stable in air and, unlike Pt, can be recovered 100 % after poisoning by carbon monoxide. Following characterization of the [NiFe]S77 electrode, a fuel cell comprising a [NiFe]S77 anode and Pt cathode was constructed and shown to have a a higher power density than that achievable by Pt.
- Published
- 2014
35. Biochemical characterization of psychrophilic Mn-superoxide dismutase from newly isolated Exiguobacterium sp. OS-77
- Author
-
Kyoshiro Nonaka, Ki Seok Yoon, and Seiji Ogo
- Subjects
Hot Temperature ,Molecular Sequence Data ,Biology ,Microbiology ,Cofactor ,Superoxide dismutase ,Bacterial Proteins ,RNA, Ribosomal, 16S ,Enzyme Stability ,Amino Acid Sequence ,Psychrophile ,Phylogeny ,Thermostability ,chemistry.chemical_classification ,Bacillales ,Strain (chemistry) ,Superoxide Dismutase ,General Medicine ,Hydrogen-Ion Concentration ,Exiguobacterium ,biology.organism_classification ,Enzyme ,chemistry ,Biochemistry ,biology.protein ,Molecular Medicine ,Dismutase - Abstract
Many types of superoxide dismutases have been purified and characterized from various bacteria, however, a psychrophilic Mn-superoxide dismutase (MnSOD) has not yet been reported. Here, we describe the purification and the biochemical characterization of the psychrophilic MnSOD from Exiguobacterium sp. strain OS-77 (EgMnSOD). According to 16S rRNA sequence analysis, a newly isolated bacterium strain OS-77 belongs to the genus Exiguobacterium. The optimum growth temperature of the strain OS-77 is 20 °C. The EgMnSOD is a homodimer of 23.5 kDa polypeptides determined by SDS-PAGE and gel filtration analysis. UV-Vis spectrum and ICP-MS analysis clearly indicated that the homogeneously purified enzyme contains only a Mn ion as a metal cofactor. The optimal reaction pH and temperature of the enzyme were pH 9.0 and 5 °C, respectively. Notably, the purified EgMnSOD was thermostable up to 45 °C and retained 50% activity after 21.2 min at 60 °C. The differential scanning calorimetry also indicated that the EgMnSOD is thermostable, exhibiting two protein denaturation peaks at 65 and 84 °C. The statistical analysis of amino acid sequence and composition of the EgMnSOD suggests that the enzyme retains psychrophilic characteristics.
- Published
- 2014
36. The effects of ankle mobilization and active stretching on the difference of weight-bearing distribution, low back pain and flexibility in pronated-foots subjects
- Author
-
Seong-Doo Park and Ki-Seok Yoon
- Subjects
musculoskeletal diseases ,Pronated-foot ,medicine.medical_specialty ,Mobilization ,Flexibility (anatomy) ,business.industry ,Visual analogue scale ,Physical Therapy, Sports Therapy and Rehabilitation ,Lumbar vertebrae ,medicine.disease_cause ,Low back pain ,Weight-bearing ,medicine.anatomical_structure ,Physical medicine and rehabilitation ,Muscle stretching exercise ,medicine ,Physical therapy ,Original Article ,Orthopedics and Sports Medicine ,Ankle ,medicine.symptom ,business ,Balance (ability) - Abstract
The purpose of this study was designed to analyze the effects mobilization and active stretching on the difference of weight-bearing distribution, low back pain, and flexibility in pronated-foot subjects. The subjects of this study were 16 chronic low back pain patients. They were randomly divided into the control and experimental group. The experimental group had used the model of ankle mobilization and calf muscle active stretching three times per week, for 4 weeks. The control group did same method without an ankle mobilization. The range of flexion and extension motion of the lumbar vertebrae and low back pain degree and difference of weight-bearing were measured before and after the experiment. The model of ankle mobilization and calf muscle stretching of pronated-foot significantly improved the range of flexion and extension motion of the vertebrae. And the visual analogue scale and distribution of weight-bearing were decreased in both of two groups. In other word, the exercise of this study showed that the model of ankle mobilization and calf muscle stretching of pronated-foot had positive effects on improving the range of flexion and extension motion of the vertebrae. The calf muscle stretching was easy and it is effective in therapy that patients by themselves and helped to recover the balance of the vertebrae to combine ankle mobilization and muscle stretching.
- Published
- 2013
37. Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F
- Author
-
Kyoshiro Nonaka, Seiji Ogo, Ki Seok Yoon, and Nga T. Nguyen
- Subjects
chemistry.chemical_classification ,Hydrogenase ,biology ,Stereochemistry ,Chemistry ,Protein subunit ,Molecular Sequence Data ,Bioengineering ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Serine ,Residue (chemistry) ,Enzyme ,Biochemistry ,Biocatalysis ,Specific activity ,Amino Acid Sequence ,Desulfovibrio vulgaris ,Oxidation-Reduction ,Sequence Alignment ,Biotechnology ,Cysteine - Abstract
[NiFeSe]hydrogenases are promising biocatalysts in H2-based technology due to their high catalytic activity and O2-stability. Here, we report purification and characterization of a new membrane-associated [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F ([NiFeSe]DvMF). The [NiFeSe]DvMF was composed of two subunits, corresponding to a large subunit of 58.3 kDa and a small subunit of 29.3 kDa determined by SDS-PAGE. Unlike conventional [NiFeSe]hydrogenases having catalytic bias toward H2-production, the [NiFeSe]DvMF showed 11-fold higher specific activity of H2-oxidation (2444 U/mg) than that of H2-production (217 U/mg). At the optimal reaction temperature of the enzyme (65°C), the specific activity of H2-oxidation could reach up to 21,553 U/mg. Amperometric assays of the [NiFeSe]DvMF clearly indicated that the enzyme had a remarkable O2-stability. According to the amino acid sequence alignment, the conserved cysteine residue at position 281 in medial cluster of other [NiFeSe]hydrogenases was specifically replaced by a serine residue (Ser281) in the [NiFeSe]DvMF. These results indicate that the [NiFeSe]DvMF can play as a new H2-oxidizing and O2-stable biocatalyst, along with providing helpful insights into the structure-function relationship of [NiFeSe]hydrogenases.
- Published
- 2013
38. O2-stable membrane-bound [NiFe]hydrogenase from a newly isolated Citrobacter sp. S-77
- Author
-
Shigenobu Eguchi, Ki Seok Yoon, and Seiji Ogo
- Subjects
chemistry.chemical_classification ,Citrobacter ,Hydrogenase ,Strain (chemistry) ,Molecular mass ,Cytochrome ,Dimer ,Cell Membrane ,Bioengineering ,Electron acceptor ,Biology ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Oxygen ,chemistry.chemical_compound ,Enzyme ,chemistry ,Biochemistry ,Enzyme Stability ,biology.protein ,Oxidation-Reduction ,Phylogeny ,Biotechnology - Abstract
Hydrogenases are of great interest due to their potential use in H(2)-based technology. However, most hydrogenases are highly sensitive to O(2), which have been the major bottleneck in hydrogenase studies. Here we report an O(2)-stable membrane-bound [NiFe]hydrogenase (MBH) purified from a newly isolated strain, S-77. According to the 16S rRNA gene sequence and phylogenetic analysis of the strain S-77, it belongs to the genus of Citrobacter. In vitro experiments using the cytoplasmic membrane of strain S-77 suggested that a cytochrome b acts as the physiological electron acceptor of the MBH. The purified MBH was composed of a dimer of heterodimers, consisting of two distinct subunits with the molecular weights of 58.5 and 38.5 kDa. The enzyme showed a specific activity for H(2)-oxidation of 661 U/mg, which is 35-fold greater than that for H(2)-production of 18.7 U/mg. Notably, the MBH showed a remarkable O(2)-stability, maintaining almost 95% of its original activity even after incubation for 30 h in air at 4°C. These results suggest that the O(2)-stable MBH may play an important role in the H(2)-metabolic pathway under the aerobic conditions of Citrobacter sp. S-77. This is the first report of the purification and biochemical characterization of an O(2)-stable MBH from the genus of Citrobacter.
- Published
- 2012
39. Purification and characterization of a highly thermostable, oxygen-resistant, respiratory [NiFe]-hydrogenase from a marine, aerobic hydrogen-oxidizing bacterium Hydrogenovibrio marinus
- Author
-
Kiyoshi Fujisawa, Ki Seok Yoon, Keiichi Fukuda, and Hirofumi Nishihara
- Subjects
chemistry.chemical_classification ,Hydrogenase ,biology ,Renewable Energy, Sustainability and the Environment ,Energy Engineering and Power Technology ,chemistry.chemical_element ,Condensed Matter Physics ,biology.organism_classification ,Oxygen ,Active center ,Nickel ,Fuel Technology ,Enzyme ,Biochemistry ,chemistry ,Oxidizing agent ,Enzyme kinetics ,Bacteria ,Nuclear chemistry - Abstract
The membrane-bound [NiFe]-hydrogenase from Hydrogenovibrio marinus (HmMBH) was purified homogeneously under anaerobic conditions. Its molecular weight was estimated as 110 kDa, consisting of a heterodimeric structure of 66 kDa and 37 kDa subunits. The purified enzyme exhibited high activity in a wide temperature range: 185 U/mg at 30 °C and 615 U/mg at 85 °C (the optimum temperature). The Km and kcat/Km values for H2 were, respectively, 12 μM and 8.58 × 107 M−1 s−1. The optimum reaction pH was 7.8, but its stability was particularly high at pH 4.0–7.0. Results show that HmMBH was remarkably thermostable and oxygen-resistant: its half-life was 75 h at 80 °C under H2, and more than 72 h at 4 °C under air. The air-oxidized HmMBH for 72 h showed only weak EPR signals of Ni–B, suggesting a structural feature in which the active center is not easily oxidized.
- Published
- 2011
40. Synthesis of Aqueous-stable and Water-soluble Mononuclear Nonheme MnV–Oxo Complexes Using H2O2 as an Oxidant
- Author
-
Hidetaka Nakai, Takahiro Kikunaga, Seiji Ogo, Takeshi Yatabe, Takahiro Matsumoto, and Ki Seok Yoon
- Subjects
chemistry.chemical_compound ,Aqueous solution ,Water soluble ,chemistry ,chemistry.chemical_element ,General Chemistry ,Manganese ,Acetonitrile ,Hydrogen peroxide ,Nuclear chemistry - Abstract
We report the synthesis of mononuclear nonheme manganese(V)–oxo complexes in aqueous acetonitrile solution from the reaction of manganese(III) complexes using hydrogen peroxide as an oxidant for th...
- Published
- 2014
41. Biochemical characterization of a bifunctional acetaldehyde-alcohol dehydrogenase purified from a facultative anaerobic bacterium Citrobacter sp. S-77
- Author
-
Seiji Ogo, Kohsei Tsuji, and Ki Seok Yoon
- Subjects
0301 basic medicine ,Octoxynol ,Acylation ,030106 microbiology ,Detergents ,Aldehyde dehydrogenase ,Bioengineering ,Dehydrogenase ,Acetaldehyde ,Applied Microbiology and Biotechnology ,Cofactor ,03 medical and health sciences ,chemistry.chemical_compound ,Citrobacter ,Acetyl Coenzyme A ,Phosphofructokinase 2 ,Coenzyme A ,Anaerobiosis ,Ethanol metabolism ,Alcohol dehydrogenase ,chemistry.chemical_classification ,biology ,Chemistry ,Alcohol Dehydrogenase ,Aldehyde Oxidoreductases ,Multifunctional Enzymes ,Betaine ,Molecular Weight ,Kinetics ,Protein Subunits ,030104 developmental biology ,Enzyme ,Biochemistry ,Solubility ,Alcohols ,biology.protein ,Biocatalysis ,Biotechnology - Abstract
Acetaldehyde-alcohol dehydrogenase (ADHE) is a bifunctional enzyme consisting of two domains of an N-terminal acetaldehyde dehydrogenase (ALDH) and a C-terminal alcohol dehydrogenase (ADH). The enzyme is known to be important in the cellular alcohol metabolism. However, the role of coenzyme A-acylating ADHE responsible for ethanol production from acetyl-CoA remains uncertain. Here, we present the purification and biochemical characterization of an ADHE from Citrobacter sp. S-77 (ADHE(S77)). Interestingly, the ADHE(S77) was unable to be solubilized from membrane with detergents either 1% Triton X-100 or 1% Sulfobetaine 3-12. However, the enzyme was easily dissociated from membrane by high-salt buffers containing either 1.0 M NaCl or (NH(4))(2)SO(4) without detergents. The molecular weight of a native protein was estimated as approximately 400 kDa, consisting of four identical subunits of 96.3 kDa. Based on the specific activity and kinetic analysis, the ADHES77 tended to have catalytic reaction towards acetaldehyde elimination rather than acetaldehyde formation. Our experimental observation suggests that the ADHES77 may play a pivotal role in modulating intracellular acetaldehyde concentration.
- Published
- 2015
42. Structural integrity evaluation for interference-fit flywheels in reactor coolant pumps of nuclear power plants
- Author
-
Taek-sang Choi, June-soo Park, Ki-seok Yoon, Jai-Hak Park, and Ha-Cheol Song
- Subjects
Engineering ,business.industry ,Mechanical Engineering ,Fracture mechanics ,Structural engineering ,Paris' law ,Flywheel ,Finite element method ,Mechanics of Materials ,Residual stress ,Fracture (geology) ,business ,Hydraulic pump ,Stress intensity factor - Abstract
This study is concerned with structural integrity evaluations for the interference-fit flywheels in reactor coolant pumps (RCPs) of nuclear power plants. Stresses in the flywheel due to the shrinkage loads and centrifugal loads at the RCP normal operation speed, design overspeed and joint-release speed are obtained using the finite element method (FEM), where release of the deformation-controlled stresses as a result of structural interactions during rotation is considered. Fracture mechanics evaluations for a series of cracks assumed to exist in the flywheel are conducted, considering ductile (fatigue) and non-ductile fracture, and stress intensity factors are obtained for the cracks using the finite element alternating method (FEAM). From analysis results, it is found that fatigue crack growth rates calculated are negligible for smaller cracks. Meanwhile, the material resistance to non-ductile fracture in terms of the critical stress intensity factor(K IC) and the nil-ductility transition reference temperature RTinNDT are governing factors for larger cracks.
- Published
- 2005
43. Characterization of the Co-Silicide Penetration Depth into the Junction Area for 0.15 and Sub-0.15 Micron CMOS Technology
- Author
-
Hee-Hwan Ji, Hi-Deok Lee, Ki-Seok Yoon, Keun-Koo Kang, Young-Jin Park, Mi-Suk Bae, Myoung-Jun Jang, Jung-Hoon Choi, Geun-Suk Park, Joo-Hyoung Lee, Key-Min Lee, and Seong-Hyun Park
- Subjects
Materials science ,Physics and Astronomy (miscellaneous) ,business.industry ,Schottky barrier ,General Engineering ,General Physics and Astronomy ,Schottky diode ,Reverse leakage current ,chemistry.chemical_compound ,CMOS ,chemistry ,Depletion region ,Silicide ,Optoelectronics ,business ,Penetration depth ,Diode - Abstract
The penetration depth of cobalt silicide layer in shallow junction is assessed using the current–voltage curve both in reverse and forward bias regions. The reverse leakage current characteristics said that silicide has affected both of the areal and peripheral intensive n+/p diodes because the leakage current is increased about one order of magnitude by silicidation. In case of p+/n junction, there is no increase of reverse leakage current. In case of forward region, however, only the forward current of peripheral intensive diode was increased by silicidation. From the different junction current behavior in forward and reverse bias region, it can be said that the penetrated depth of silicide layer is almost near to the space charge region but not into it for area diode. However, in case of peripheral intensive diode, silicide has penetrated into the space charge region. The Schottky contact area formed by silicide penetration is extracted as 3.02 µm2. The extracted Schottky barrier for n+/p parameter diode is 0.63 eV which is quite similar to the theoretical value of 0.64 eV.
- Published
- 2002
44. Cover Feature: A Fusion of Biomimetic Fuel and Solar Cells Based on Hydrogenase, Photosystem II, and Cytochrome c Oxidase (ChemCatChem 21/2017)
- Author
-
Mitsuhiro Kikkawa, Ki-Seok Yoon, Seiji Ogo, Kenji Kaneko, Takeshi Yatabe, Takao Enomoto, Takahiro Matsumoto, and Suzuki Kazuharu
- Subjects
Fusion ,Hydrogenase ,Photosystem II ,biology ,Chemistry ,Organic Chemistry ,chemistry.chemical_element ,Photochemistry ,Catalysis ,Inorganic Chemistry ,Feature (computer vision) ,biology.protein ,Fuel cells ,Cytochrome c oxidase ,Cover (algebra) ,Iridium ,Physical and Theoretical Chemistry - Published
- 2017
45. Cover Picture: One Model, Two Enzymes: Activation of Hydrogen and Carbon Monoxide (Angew. Chem. Int. Ed. 33/2017)
- Author
-
Ki-Seok Yoon, Yuki Mori, Hideki Hayashi, Takahiro Matsumoto, Tatsuya Ando, Seiji Ogo, Masashi Asano, and Takeshi Yatabe
- Subjects
chemistry.chemical_classification ,Hydrogenase ,Hydrogen ,INT ,chemistry.chemical_element ,Dehydrogenase ,Bioinorganic chemistry ,General Chemistry ,Catalysis ,chemistry.chemical_compound ,Enzyme ,chemistry ,Organic chemistry ,Cover (algebra) ,Carbon monoxide - Published
- 2017
46. Titelbild: One Model, Two Enzymes: Activation of Hydrogen and Carbon Monoxide (Angew. Chem. 33/2017)
- Author
-
Ki-Seok Yoon, Tatsuya Ando, Seiji Ogo, Yuki Mori, Takahiro Matsumoto, Masashi Asano, Hideki Hayashi, and Takeshi Yatabe
- Subjects
chemistry.chemical_classification ,chemistry.chemical_compound ,Enzyme ,chemistry ,Hydrogen ,chemistry.chemical_element ,Organic chemistry ,General Medicine ,Carbon monoxide - Published
- 2017
47. A [NiFe]hydrogenase model that catalyses the release of hydrogen from formic acid
- Author
-
Seiji Ogo, Takahiro Matsumoto, Nga T. Nguyen, Ki Seok Yoon, Yuki Mori, Ryota Kabe, Takeshi Yatabe, and Hidetaka Nakai
- Subjects
Models, Molecular ,Hydrogenase ,Hydrogen ,Formates ,Formic acid ,Inorganic chemistry ,chemistry.chemical_element ,Catalysis ,chemistry.chemical_compound ,Materials Chemistry ,Metals and Alloys ,General Chemistry ,Carbon Dioxide ,Hydrogen-Ion Concentration ,Combinatorial chemistry ,Decomposition ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,chemistry ,Models, Chemical ,Carbon dioxide ,Ceramics and Composites ,Biocatalysis ,NiFe hydrogenase - Abstract
We report the decomposition of formic acid to hydrogen and carbon dioxide, catalysed by a NiRu complex originally developed as a [NiFe]hydrogenase model. This is the first example of H2 evolution, catalysed by a [NiFe]hydrogenase model, which does not require additional energy.
- Published
- 2014
48. Synthesis and crystal structure of a dinuclear, monomeric Mn(II) p-semiquinonato complex
- Author
-
Ki Seok Yoon, Takeshi Yatabe, Harutaka Nakamori, Takahiro Matsumoto, Hidetaka Nakai, and Seiji Ogo
- Subjects
inorganic chemicals ,Solid-state chemistry ,Photosystem II ,Inorganic chemistry ,Molecular Conformation ,chemistry.chemical_element ,macromolecular substances ,Crystal structure ,Crystallography, X-Ray ,Oxygen ,Catalysis ,chemistry.chemical_compound ,Coordination Complexes ,Polymer chemistry ,Materials Chemistry ,Benzoquinones ,Reactivity (chemistry) ,Manganese ,Metals and Alloys ,Photosystem II Protein Complex ,General Chemistry ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Monomer ,chemistry ,Ceramics and Composites ,Oxidation-Reduction - Abstract
Herein, we report the first crystal structure of a monomeric p-semiquinonato d-block complex and its reactivity toward dioxygen, closely associated with a biological system of an oxygen evolving centre of photosystem II.
- Published
- 2014
49. Molybdenum-containing membrane-bound formate dehydrogenase isolated from Citrobacter sp. S-77 having high stability against oxygen, pH, and temperature
- Author
-
Ki Seok Yoon, Takeshi Yatabe, Seiji Ogo, and Nga T. Nguyen
- Subjects
Stereochemistry ,Protein subunit ,Molecular Sequence Data ,Bioengineering ,Formate dehydrogenase ,Applied Microbiology and Biotechnology ,Formate oxidation ,chemistry.chemical_compound ,Citrobacter ,Bacterial Proteins ,Enzyme Stability ,Amino Acid Sequence ,Thermostability ,chemistry.chemical_classification ,Molybdenum ,biology ,Molecular mass ,Chemistry ,Temperature ,Electron acceptor ,Hydrogen-Ion Concentration ,biology.organism_classification ,Formate Dehydrogenases ,Molecular Weight ,Oxygen ,Heme B ,Kinetics ,Protein Subunits ,Biochemistry ,Oxidation-Reduction ,Sequence Alignment ,Biotechnology - Abstract
Membrane-bound formate dehydrogenase (FDH) was purified to homogeneity from a facultative anaerobic bacterium Citrobacter sp. S-77. The FDH from Citrobacter sp. S-77 (FDHS77) was a monomer with molecular mass of approximately 150 kDa. On SDS-PAGE, the purified FDHS77 showed as three different protein bands with molecular mass of approximately 95, 87, and 32 kDa, respectively. Based on the N-terminal amino acid sequence analysis, the sequence alignments observed for the 87 kDa protein band were identical to that of the large subunit of 95 kDa, indicating that the purified FDHS77 consisted of two subunits; a 95 kDa large subunit and a 32 kDa small subunit. The purified FDHS77 in this purification did not contain a heme b subunit, but the FDHS77 showed significant activity for formate oxidation, determined by the Vmax of 30.4 U/mg using benzyl viologen as an electron acceptor. The EPR and ICP-MS spectra indicate that the FDHS77 is a molybdenum-containing enzyme, displaying a remarkable O2-stability along with thermostability and pH resistance. This is the first report of the purification and characterization of a FDH from Citrobacter species.
- Published
- 2014
50. Rubredoxin from the Green Sulfur Bacterium Chlorobium tepidum Functions as an Electron Acceptor for Pyruvate Ferredoxin Oxidoreductase
- Author
-
Craig Hemann, F. Robert Tabita, Ki Seok Yoon, and Russ Hille
- Subjects
Pyruvate decarboxylation ,Circular dichroism ,Pyruvate Synthase ,Stereochemistry ,Electrons ,Photochemistry ,Biochemistry ,law.invention ,Chlorobi ,law ,Rubredoxin ,Electron paramagnetic resonance ,Molecular Biology ,Ferredoxin ,chemistry.chemical_classification ,Pyruvate synthase ,biology ,Circular Dichroism ,Rubredoxins ,Electron Spin Resonance Spectroscopy ,Ketone Oxidoreductases ,Cell Biology ,Electron acceptor ,Chromatography, Ion Exchange ,biology.organism_classification ,Chlorobium tepidum ,chemistry ,biology.protein ,Electrophoresis, Polyacrylamide Gel ,Spectrophotometry, Ultraviolet - Abstract
Rubredoxin (Rd) from the moderately thermophilic green sulfur bacterium Chlorobium tepidum was found to function as an electron acceptor for pyruvate ferredoxin oxidoreductase (PFOR). This enzyme, which catalyzes the conversion of pyruvate to acetyl-CoA and CO(2), exhibited an absolute dependence upon the presence of Rd. However, Rd was incapable of participating in the pyruvate synthase or CO(2) fixation reaction of C. tepidum PFOR, for which two different reduced ferredoxins are employed as electron donors. These results suggest a specific functional role for Rd in pyruvate oxidation and provide the initial indication that the two important physiological reactions catalyzed by PFOR/pyruvate synthase are dependent on different electron carriers in the cell. The UV-visible spectrum of oxidized Rd, with a monomer molecular weight of 6500, gave a molar absorption coefficient at 492 nm of 6.89 mM(-1) cm(-1) with an A(492)/A(280) ratio of 0.343 and contained one iron atom/molecule. Further spectroscopic studies indicated that the CD spectrum of oxidized C. tepidum Rd exhibited a unique absorption maximum at 385 nm and a shoulder at 420 nm. The EPR spectrum of oxidized Rd also exhibited unusual anisotropic resonances at g = 9.675 and g = 4.322, which is composed of a narrow central feature with broader shoulders to high and low field. The midpoint reduction potential of C. tepidum Rd was determined to be -87 mV, which is the most electronegative value reported for Rd from any source.
- Published
- 1999
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.