63 results on '"Hulin Tai"'
Search Results
2. Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77
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Takahiro Imanishi, Koji Nishikawa, Midori Taketa, Katsuhiro Higuchi, Hulin Tai, Shun Hirota, Hironobu Hojo, Toru Kawakami, Kiriko Hataguchi, Kayoko Matsumoto, Hideaki Ogata, and Yoshiki Higuchi
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Models, Molecular ,Carbon Monoxide ,Protein Conformation ,Electron Spin Resonance Spectroscopy ,Biophysics ,Crystallography, X-Ray ,Condensed Matter Physics ,Biochemistry ,Research Communications ,Citrobacter ,Bacterial Proteins ,Hydrogenase ,Structural Biology ,Catalytic Domain ,Spectroscopy, Fourier Transform Infrared ,Genetics ,Enzyme Inhibitors - Abstract
Hydrogenases catalyze the reversible oxidation of H2. Carbon monoxide (CO) is known to be a competitive inhibitor of O2-sensitive [NiFe]-hydrogenases. Although the activities of some O2-tolerant [NiFe]-hydrogenases are unaffected by CO, the partially O2-tolerant [NiFe]-hydrogenase from Citrobacter sp. S-77 (S77-HYB) is inhibited by CO. In this work, the CO-bound state of S77-HYB was characterized by activity assays, spectroscopic techniques and X-ray crystallography. Electron paramagnetic resonance spectroscopy showed a diamagnetic Ni2+ state, and Fourier-transform infrared spectroscopy revealed the stretching vibration of the exogenous CO ligand. The crystal structure determined at 1.77 Å resolution revealed that CO binds weakly to the nickel ion in the Ni–Fe active site of S77-HYB. These results suggest a positive correlation between O2 and CO tolerance in [NiFe]-hydrogenases.
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- 2022
3. Construction of 'peptide-hemin/DNA' hybrid-complexes and their peroxidase activities
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Jing Liu, Taozhe Zhang, Jinyang Feng, Cui Yue, Li Zhang, Yunong Wang, Meiyu Cui, Donghao Li, and Hulin Tai
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Materials Chemistry ,Metals and Alloys ,Ceramics and Composites ,General Chemistry ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
N-acetylated microperoxidase-11 and G-quadruplex DNA are shown to form a stable “peptide-hemin/DNA” hybrid-complex, in which the peroxidase activity at the interface between hemin and G-quartet planes exponentially increase with increasing...
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- 2023
4. Proton Transfer Mechanisms in Bimetallic Hydrogenases
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Sven T. Stripp, Hulin Tai, and Shun Hirota
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Iron-Sulfur Proteins ,Coordination sphere ,Light ,Infrared spectroscopy ,Protonation ,010402 general chemistry ,01 natural sciences ,Redox ,Electron transfer ,Hydrogenase ,biophysics ,Catalytic Domain ,Carbon Monoxide ,biology ,010405 organic chemistry ,Hydride ,Chemistry ,Active site ,Hydrogen Bonding ,Bioinorganic chemistry ,General Medicine ,General Chemistry ,0104 chemical sciences ,Crystallography ,biology.protein ,Protons ,Oxidation-Reduction ,Hydrogen - Abstract
Hydrogenases are iron-sulfur enzymes that catalyze proton reduction and H2 oxidation with outstanding efficiency. They are considered blueprints for the design of transition metal complexes, e.g. as heterogenous catalysts in the context of H2 production from water. Moreover, hydrogenases are biological model systems for metal hydride chemistry and proton-coupled electron transfer. Depending on the composition of the active site cofactor, [NiFe]-hydrogenases are distinguished from [FeFe]-hydrogenases. The former binds a hetero bimetallic nickel/iron site, embedded in the protein by four cysteine ligands. The later, by contrast, carries a homo bimetallic iron/iron site attached to the protein by only a single cysteine. Carbon monoxide and cyanide ligands (CO/CN) at the active site facilitated detailed investigations of hydrogenase catalysis by infrared spectroscopy, owing to strong signals and redox-dependent frequency shifts. However, the details of proton transfer have not been addressed experimentally.We found that specific redox state transitions in [NiFe]- and [FeFe]-hydrogenase can be triggered by visible light to record extremely sensitive ‘light-minus-dark’ infrared difference spectra monitoring key amino acid residues as shown in the ToC figure. As these transitions are coupled to protonation changes, our data allowed investigating dynamic hydrogen-bonding changes that go well beyond the resolution of protein crystallography. In [NiFe]-hydrogenase, photolysis of the bridging hydride ligand in the ‘Ni-C’ state was followed by rapid accumulation of the ‘Ni-SIa’ state and/or ‘Ni-L’ state. Infrared difference spectra in various isotopic media clearly indicated the formation of a protonated cysteine residue as well as hydrogen-bonding changes involving the COOH group of a glutamic acid residue and a ‘dangling water’ molecule. These findings are in excellent agreement with crystallographic analyses of [NiFe]-hydrogenase in the Ni-R state and allowed devising a molecular precise model of catalytic proton transfer. In [FeFe]-hydrogenase, an external redox dye was used to accumulate the ‘Hred’ state over the oxidized resting state ‘Hox’. Infrared difference spectra of wild-type enzyme and numerous amino acid variants indicated hydrogen-bonding changes involving the COOH groups of two glutamic acid residues. Moreover, we noted the deprotonation of an arginine residue. Crystallographic analyses of [FeFe]-hydrogenase in the Hox state failed to explain the rapid proton transfer due to a ‘breach’ in the succession of residues. To this end, our findings facilitated a molecular precise model of ‘discontinued’ proton transfer.The comparison of catalytic proton transfer in bimetallic hydrogenases emphasizes the role of the outer coordination sphere. We suggest that the stable protonation of a nickel-ligating cysteine in [NiFe]-hydrogenase has a crucial influence on the preferred direction of proton flow and catalysis (i.e., H2 oxidation). On the contrary, proton transfer in [FeFe]-hydrogenase involves an adjacent cysteine as a relay group that promotes both proton release and proton uptake. We presume that this causes the notable bidirectionality of [FeFe]-hydrogenase. These observations must guide the design of biomimetic compounds for the production or consumption of H2.
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- 2020
5. Mechanism and Application of the Catalytic Reaction of [NiFe] Hydrogenase: Recent Developments
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Shun Hirota and Hulin Tai
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Iron-Sulfur Proteins ,Reaction mechanism ,Hydrogenase ,Bioelectric Energy Sources ,Archaeal Proteins ,Electrons ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Redox ,Heterolysis ,Catalysis ,Bacterial Proteins ,Catalytic Domain ,Solar Energy ,Humans ,Desulfovibrio vulgaris ,Molecular Biology ,biology ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,Active site ,Solar fuel ,Combinatorial chemistry ,0104 chemical sciences ,Biocatalysis ,biology.protein ,Molecular Medicine ,Cupriavidus necator ,Methanosarcina barkeri ,Protons ,Desulfovibrio gigas ,Hydrophobic and Hydrophilic Interactions ,Oxidation-Reduction ,Hydrogen - Abstract
Hydrogenases (H2 ase) catalyze the oxidation of dihydrogen and the reduction of protons with remarkable efficiency, thereby attracting considerable attention in the energy field due to their biotechnological potential. For this simple reaction, [NiFe] H2 ase has developed a sophisticated but intricate mechanism with the heterolytic cleavage of dihydrogen, where its Ni-Fe active site exhibits various redox states. Recently, new spectroscopic and crystal structure studies of [NiFe] H2 ases have been reported, providing significant insights into the catalytic reaction mechanism, hydrophobic gas-access tunnel, proton-transfer pathway, and electron-transfer pathway of [NiFe] H2 ases. In addition, [NiFe] H2 ases have been shown to play an important role in biofuel cell and solar dihydrogen production. This concept provides an overview of the biocatalytic reaction mechanism and biochemical application of [NiFe] H2 ases based on the new findings.
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- 2020
6. Redox-dependent conformational changes of a proximal [4Fe–4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2
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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
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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
7. Activation Mechanism of the Streptomyces Tyrosinase Assisted by the Caddie Protein
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Naohiko Bando, Yasuyuki Matoba, Shogo Kihara, Shun Hirota, Miyuki Sakaguchi, Masanori Sugiyama, Teruo Kuroda, Hulin Tai, Takashi Ogura, Yoshimi Muraki, Hironari Yoshitsu, and Kure'e Kayama
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Models, Molecular ,0301 basic medicine ,Reducing agent ,Stereochemistry ,Tyrosinase ,01 natural sciences ,Biochemistry ,Streptomyces ,Active center ,Protein Aggregates ,03 medical and health sciences ,Residue (chemistry) ,Apoenzymes ,Bacterial Proteins ,Catalytic Domain ,Benzoquinones ,Binding site ,chemistry.chemical_classification ,Binding Sites ,biology ,Monophenol Monooxygenase ,010405 organic chemistry ,Chemistry ,biology.organism_classification ,Recombinant Proteins ,Dihydroxyphenylalanine ,0104 chemical sciences ,Quinone ,Enzyme Activation ,030104 developmental biology ,Enzyme ,Amino Acid Substitution ,Solubility ,Reducing Agents ,Mutation ,Tyrosine ,Protein Multimerization ,Carrier Proteins ,Oxidation-Reduction ,Copper - Abstract
Tyrosinase (EC 1.14.18.1), which possesses two copper ions at the active center, catalyzes a rate-limiting reaction of melanogenesis, that is, the conversion of a phenol to the corresponding ortho-quinone. The enzyme from the genus Streptomyces is generated as a complex with a “caddie” protein that assists the transport of two copper ions into the active center. In this complex, the Tyr98 residue in the caddie protein was found to be accommodated in the pocket of the active center of tyrosinase, probably in a manner similar to that of l-tyrosine as a genuine substrate of tyrosinase. Under physiological conditions, the addition of the copper ion to the complex releases tyrosinase from the complex, in accordance with the aggregation of the caddie protein. The release of the copper-bound tyrosinase was found to be accelerated by adding reducing agents under aerobic conditions. Mass spectroscopic analysis indicated that the Tyr98 residue was converted to a reactive quinone, and resonance Raman spectroscopic a...
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- 2017
8. Structural basis of the redox switches in the NAD + -reducing soluble [NiFe]-hydrogenase
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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
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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
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- 2017
9. Characterization of the interaction between heme and a parallel G-quadruplex DNA formed from d(TTGAGG)
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Yusaku Nakayama, Yusuke Nakano, Yasuhiko Yamamoto, Tomokazu Shibata, Yuya Katahira, Yuki Moritaka, and Hulin Tai
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Models, Molecular ,0301 basic medicine ,Stereochemistry ,Proton Magnetic Resonance Spectroscopy ,Oligonucleotides ,Biophysics ,Stacking ,Heme ,Nucleic Acid Denaturation ,010402 general chemistry ,G-quadruplex ,01 natural sciences ,Biochemistry ,Adduct ,Structure-Activity Relationship ,03 medical and health sciences ,chemistry.chemical_compound ,Moiety ,Protein Interaction Domains and Motifs ,Molecular Biology ,Carbon Monoxide ,Binding Sites ,Temperature ,Porphyrin ,0104 chemical sciences ,G-Quadruplexes ,030104 developmental biology ,chemistry ,DNA ,Protein Binding ,Carbon monoxide - Abstract
Structure-function relationships of complexes between heme and G-quadruplex DNAs have attracted interest from researchers in related fields. A carbon monoxide adduct of a complex between heme and a parallel G-quadruplex DNA formed from hexanucleotide d(TTGAGG) (heme-[d(TTGAGG)]4 complex) has been characterized using 1H NMR spectroscopy, and the obtained results were compared with those for the heme-[d(TTAGGG)]4 complex previously studied in order to elucidate the effect of the incorporation of an A-quartet into stacked G-quartets in the 3'-terminal region of the DNA on the structure of the heme-DNA complex. We found that a π-π stacking interaction between the porphyrin moiety of the heme and the 3'-terminal G-quartet of the DNA is affected by the nature of the stacked G-quartets. This finding provides novel insights as to the design of the molecular architecture of a heme-DNA complex. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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- 2017
10. Equilibrium between inactive ready Ni-SIr and active Ni-SIa states of [NiFe] hydrogenase studied by utilizing Ni-SIr-to-Ni-SIa photoactivation
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Yoshiki Higuchi, Koji Nishikawa, Hulin Tai, Shun Hirota, and Liyang Xu
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Hydrogenase ,010405 organic chemistry ,Chemistry ,Metals and Alloys ,Light irradiation ,General Chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Kinetic isotope effect ,Materials Chemistry ,Ceramics and Composites ,NiFe hydrogenase - Abstract
Previously, the Ni-SIr state of [NiFe] hydrogenase was found to convert to the Ni-SIa state by light irradiation. Herein, large activation energies and a large kinetic isotope effect were obtained for the reconversion of the Ni-SIa state to the Ni-SIr state after the Ni-SIr-to-Ni-SIa photoactivation, suggesting that the Ni-SIa state reacts with H2O and leaves a bridging hydroxo ligand for the Ni-SIr state.
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- 2017
11. Cysteine SH and Glutamate COOH Contributions to [NiFe] Hydrogenase Proton Transfer Revealed by Highly Sensitive FTIR Spectroscopy
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Shun Hirota, Koji Nishikawa, Hulin Tai, Zong-Wan Mao, and Yoshiki Higuchi
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Hydrogenase ,Proton ,biocatalysis ,proton transfer ,Infrared spectroscopy ,Glutamic Acid ,Protonation ,010402 general chemistry ,01 natural sciences ,Catalysis ,Electron transfer ,Deprotonation ,Spectroscopy, Fourier Transform Infrared ,Molecule ,Humans ,Cysteine ,Fourier transform infrared spectroscopy ,010405 organic chemistry ,Chemistry ,General Chemistry ,General Medicine ,0104 chemical sciences ,Crystallography ,IR spectroscopy ,hydrogen ,Protons - Abstract
A [NiFe] hydrogenase (H2 ase) is a proton-coupled electron transfer enzyme that catalyses reversible H2 oxidation; however, its fundamental proton transfer pathway remains unknown. Herein, we observed the protonation of Cys546-SH and Glu34-COOH near the Ni-Fe site with high-sensitivity infrared difference spectra by utilizing Ni-C-to-Ni-L and Ni-C-to-Ni-SIa photoconversions. Protonated Cys546-SH in the Ni-L state was verified by the observed SH stretching frequency (2505 cm-1 ), whereas Cys546 was deprotonated in the Ni-C and Ni-SIa states. Glu34-COOH was double H-bonded in the Ni-L state, as determined by the COOH stretching frequency (1700 cm-1 ), and single H-bonded in the Ni-C and Ni-SIa states. Additionally, a stretching mode of an ordered water molecule was observed in the Ni-L and Ni-C states. These results elucidate the organized proton transfer pathway during the catalytic reaction of a [NiFe] H2 ase, which is regulated by the H-bond network of Cys546, Glu34, and an ordered water molecule.
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- 2019
12. Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O
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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
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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
13. Comprehensive reaction mechanisms at and near the Ni–Fe active sites of [NiFe] hydrogenases
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Yoshiki Higuchi, Shun Hirota, and Hulin Tai
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Reaction mechanism ,Hydrogenase ,Electrons ,Crystallography, X-Ray ,010402 general chemistry ,01 natural sciences ,Heterolysis ,Redox ,Catalysis ,Reversible reaction ,Inorganic Chemistry ,Catalytic Domain ,Acid-Base Equilibrium ,biology ,010405 organic chemistry ,Hydride ,Chemistry ,Active site ,0104 chemical sciences ,Crystallography ,biology.protein ,Thermodynamics ,Protons ,Oxidation-Reduction ,Hydrogen - Abstract
[NiFe] hydrogenase (H2ase) catalyzes the oxidation of dihydrogen to two protons and two electrons and/or its reverse reaction. For this simple reaction, the enzyme has developed a sophisticated but intricate mechanism with heterolytic cleavage of dihydrogen (or a combination of a hydride and a proton), where its Ni–Fe active site exhibits various redox states. Recently, thermodynamic parameters of the acid–base equilibrium for activation–inactivation, a new intermediate in the catalytic reaction, and new crystal structures of [NiFe] H2ases have been reported, providing significant insights into the activation–inactivation and catalytic reaction mechanisms of [NiFe] H2ases. This Perspective provides an overview of the reaction mechanisms of [NiFe] H2ases based on these new findings.
- Published
- 2018
14. Characterization of the Interaction between Heme and a Parallel G-Quadruplex DNA Formed from d(TTAGGGT)
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Kaori Saito, Masashi Kinoshita, Hulin Tai, Tomokazu Shibata, Yasuhiko Yamamoto, and Haruna Shimizu
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chemistry.chemical_compound ,chemistry ,Stereochemistry ,Molecule ,heterocyclic compounds ,General Chemistry ,Electronic structure ,G-quadruplex ,Heme ,DNA ,Characterization (materials science) - Abstract
The molecular structure and heme electronic structure of a complex (heme–(d(TTAGGGT))4 complex) between heme and a parallel G-quadruplex DNA formed from heptanucleotide d(TTAGGGT), i.e., (d(TTAGGGT...
- Published
- 2015
15. FT-IR Characterization of the Light-Induced Ni-L2 and Ni-L3 States of [NiFe] Hydrogenase from Desulfovibrio vulgaris Miyazaki F
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Yoshiki Higuchi, Koji Nishikawa, Seiya Inoue, Shun Hirota, and Hulin Tai
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Hydrogenase ,Light ,Protonation ,Photochemistry ,Redox ,Spectral line ,law.invention ,Deprotonation ,Nickel ,law ,Spectroscopy, Fourier Transform Infrared ,Organometallic Compounds ,Materials Chemistry ,Desulfovibrio vulgaris ,Physical and Theoretical Chemistry ,Electron paramagnetic resonance ,Spectroscopy ,biology ,Chemistry ,Electron Spin Resonance Spectroscopy ,biology.organism_classification ,Surfaces, Coatings and Films ,Crystallography ,Thermodynamics - Abstract
Different light-induced Ni-L states of [NiFe] hydrogenase from its Ni-C state have previously been observed by EPR spectroscopy. Herein, we succeeded in detecting simultaneously two Ni-L states of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F by FT-IR spectroscopy. A new light-induced νCO band at 1890 cm(-1) and νCN bands at 2034 and 2047 cm(-1) were detected in the FT-IR spectra of the H2-activated enzyme under N2 atmosphere at basic conditions, in addition to the 1910 cm(-1) νCO band and 2047 and 2061 cm(-1) νCN bands of the Ni-L2 state. The new bands were attributed to the Ni-L3 state by comparison of the FT-IR and EPR spectra. The νCO and νCN frequencies of the Ni-L3 state are the lowest frequencies observed among the corresponding frequencies of standard-type [NiFe] hydrogenases in various redox states. These results indicate that a residue, presumably Ni-coordinating Cys546, is protonated and deprotonated in the Ni-L2 and Ni-L3 states, respectively. Relatively small ΔH (6.4 ± 0.8 kJ mol(-1)) and ΔS (25.5 ± 10.3 J mol(-1) K(-1)) values were obtained for the conversion from the Ni-L2 to Ni-L3 state, which was in agreement with the previous proposals that deprotonation of Cys546 is important for the catalytic reaction of the enzyme.
- Published
- 2015
16. Equilibrium between inactive ready Ni-SI
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Hulin, Tai, Liyang, Xu, Koji, Nishikawa, Yoshiki, Higuchi, and Shun, Hirota
- Abstract
Previously, the Ni-SI
- Published
- 2017
17. Control of the Transition between Ni-C and Ni-SIa States by the Redox State of the Proximal Fe-S Cluster in the Catalytic Cycle of [NiFe] Hydrogenase
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Masayuki Suzuki, Koji Nishikawa, Shun Hirota, Yoshiki Higuchi, and Hulin Tai
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Iron-Sulfur Proteins ,Hydrogenase ,biology ,biocatalysis ,Chemistry ,Active site ,Infrared spectroscopy ,General Chemistry ,General Medicine ,Photochemistry ,Redox ,Catalysis ,iron-sulfur clusters ,law.invention ,hydrogenases ,Catalytic cycle ,Biocatalysis ,law ,IR spectroscopy ,biology.protein ,Cluster (physics) ,Electron paramagnetic resonance ,Oxidation-Reduction ,EPR spectroscopy - Abstract
[NiFe] hydrogenase catalyzes the reversible cleavage of H2. The electrons produced by the H2 cleavage pass through three Fe-S clusters in [NiFe] hydrogenase to its redox partner. It has been reported that the Ni-SI(a), Ni-C, and Ni-R states of [NiFe] hydrogenase are involved in the catalytic cycle, although the mechanism and regulation of the transition between the Ni-C and Ni-SI(a) states remain unrevealed. In this study, the FT-IR spectra under light irradiation at 138-198 K show that the Ni-L state of [NiFe] hydrogenase is an intermediate between the transition of the Ni-C and Ni-SI(a) states. The transition of the Ni-C state to the Ni-SI(a) state occurred when the proximal [Fe4S4]p(2+/+) cluster was oxidized, but not when it was reduced. These results show that the catalytic cycle of [NiFe] hydrogenase is controlled by the redox state of its [Fe4S4]p(2+/+) cluster, which may function as a gate for the electron flow from the NiFe active site to the redox partner.
- Published
- 2014
18. Effect of the Electron Density of the Heme Fe Atom on the Fe–Histidine Coordination Bond in Deoxy Myoglobin
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Sachiko Yanagisawa, Yasuhiko Yamamoto, Tomokazu Shibata, Akihiro Suzuki, Hulin Tai, Takashi Ogura, Izumi Ishigami, Ryu Nishimura, and Saburo Neya
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Crystallography ,chemistry.chemical_compound ,Electron density ,Proton ,Myoglobin ,Chemistry ,Atom ,General Chemistry ,Photochemistry ,Heme ,Histidine - Abstract
The stretching frequency of the coordination bond between the heme Fe atom and proximal histidine (His93) Ne atom (νFe–His), and the NMR shift of the His93NδH proton (His93NδH shift) of the deoxy f...
- Published
- 2014
19. Structural characterization of imidazole adducts of heme-DNA complexes
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Kaori Saito, Yasuhiko Yamamoto, Tomokazu Shibata, Akihiro Suzuki, Masashi Kinoshita, Yasuhito Suzuki, and Hulin Tai
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chemistry.chemical_compound ,Circular dichroism ,Trifluoromethyl ,Chemistry ,Stereochemistry ,Stacking ,Imidazole ,General Chemistry ,Ternary operation ,Heme ,DNA ,Adduct - Abstract
Ternary complexes composed of protoheme (heme( Fe 3+)) or 13,17-bis(2-carboxylatoethyl)-3,7-diethyl-12,18-trimethyl-2,8-ditrifluoromethylporphyrinatoiron(III) (2,8-DPF( Fe 3+)), a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), and imidazole (Im), in a ratio of 1:1:1, were prepared and their structures were characterized using optical, circular dichroism, and NMR spectroscopies. The study revealed that heme( Fe 3+) and 2,8-DPF( Fe 3+) stack onto the 3′-terminal G-quartet of the G-quadruplex DNA, ~0.4 nm apart, and that Im is coordinated to the Fe atom on the side of the heme opposite to the G-quartet in the complex. The stacking of the pseudo-C2 symmetric heme( Fe 3+) onto the C4 symmetric G-quartet in the complex resulted in the formation of two isomers with heme orientations differing by 180° about the pseudo-C2 axis, with respect to the DNA. The Im affinity of the 2,8-DPF( Fe 3+)-DNA complex was higher by a factor of ~2 than that of the heme( Fe 3+)-DNA one, which is possibly due to the stronger ligand-to-metal π donation in the 2,8-DPF( Fe 3+) as a result of a decrease in the electron density of the heme Fe atom caused by substitution of the two strongly electron-withdrawing trifluoromethyl groups.
- Published
- 2014
20. Electronic Control of Discrimination between O2 and CO in Myoglobin Lacking the Distal Histidine Residue
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Kiyohiro Imai, Saburo Neya, Takashi Matsuo, Tomokazu Shibata, Takashi Ogura, Satoshi Nagao, Izumi Ishigami, Ryu Nishimura, Hulin Tai, Osami Shoji, Akihiro Suzuki, Yasuhiko Yamamoto, Shun Hirota, and Yoshihito Watanabe
- Subjects
Stereochemistry ,Mutant ,Electrons ,Heme ,Vibration ,Cofactor ,Substrate Specificity ,Inorganic Chemistry ,chemistry.chemical_compound ,Mutant protein ,Animals ,Histidine ,Reactivity (chemistry) ,Physical and Theoretical Chemistry ,Carbon Monoxide ,biology ,Myoglobin ,Oxygen ,chemistry ,Mutation ,biology.protein ,Mutant Proteins ,Carbon monoxide - Abstract
We analyzed the oxygen (O2) and carbon monoxide (CO) binding properties of the H64L mutant of myoglobin reconstituted with chemically modified heme cofactors possessing a heme Fe atom with a variety of electron densities, in order to elucidate the effect of the removal of the distal His64 on the control of both the O2 affinity and discrimination between O2 and CO of the protein by the intrinsic heme Fe reactivity through the electron density of the heme Fe atom (ρFe). The study revealed that, as in the case of the native protein, the O2 affinity of the H64L mutant protein is regulated by the ρFe value in such a manner that the O2 affinity of the protein decreases, due to an increase in the O2 dissociation rate constant, with a decrease in the ρFe value, and that the O2 affinities of the mutant and native proteins are affected comparably by a given change in the ρFe value. On the other hand, the CO affinity of the H64L mutant protein was found to increase, due to a decrease in the CO dissociation rate constant, with a decrease in the ρFe value, whereas that of the native protein was essentially independent of a change in the ρFe value. As a result, the regulation of the O2/CO discrimination in the protein through the ρFe value is affected by the distal His64. Thus, the study revealed that the electronic tuning of the intrinsic heme Fe reactivity through the ρFe value plays a vital role in the regulation of the protein function, as the heme environment furnished by the distal His64 does.
- Published
- 2013
21. Relationship between the Electron Density of the Heme Fe Atom and the Vibrational Frequencies of the Fe-Bound Carbon Monoxide in Myoglobin
- Author
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Shun Hirota, Izumi Ishigami, Ryu Nishimura, Tomokazu Shibata, Yasuhiko Yamamoto, Hulin Tai, Takashi Ogura, Kiyohiro Imai, Saburo Neya, Takashi Matsuo, Satoshi Nagao, and Akihiro Suzuki
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Carbon Monoxide ,Electron density ,biology ,Myoglobin ,Iron ,Kinetics ,Electrons ,Heme ,Electron ,Photochemistry ,Vibration ,Cofactor ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,chemistry ,biology.protein ,Side chain ,Animals ,Physical and Theoretical Chemistry ,Carbon monoxide - Abstract
We analyzed the vibrational frequencies of the Fe-bound carbon monoxide (CO) of myoglobin reconstituted with a series of chemically modified heme cofactors possessing a heme Fe atom with a variety of electron densities. The study revealed that the stretching frequency of Fe-bound CO (ν(CO)) increases with decreasing electron density of the heme Fe atom (ρ(Fe)). This finding demonstrated that the ν(CO) value can be used as a sensitive measure of the ρ(Fe) value and that the π back-donation of the heme Fe atom to CO is affected by the heme π-system perturbation induced through peripheral side chain modifications.
- Published
- 2013
22. Control of the stability of Hydrogenobacter thermophilus cytochrome c552 through alteration of the basicity of the N-terminal amino group of the polypeptide chain
- Author
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Hulin Tai, Munegumi, Toratane, and Yamamoto, Yasuhiko
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Gene mutations -- Analysis ,Polypeptides -- Structure ,Polypeptides -- Chemical properties ,Polypeptides -- Thermal properties ,Protein folding -- Analysis ,Bacteria, Thermophilic -- Physiological aspects ,Bacteria, Thermophilic -- Genetic aspects ,Chemistry - Published
- 2010
23. Effect of heme modification on oxygen affinity of myoglobin and equilibrium of the acid-alkaline transition in metmyoglobin
- Author
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Shibata, Tomokazu, Nagao, Satoshi, Fukaya, Masashi, Hulin Tai, Nagatomo, Shigenori, Morihashi, Kenji, Matsuo, Takashi, Hirota, Shun, Suzuki, Akihiro, Imai, Kiyohiro, and Yamamoto, Yasuhiko
- Subjects
Fluorocarbons -- Structure ,Fluorocarbons -- Chemical properties ,Fluorocarbons -- Electric properties ,Heme -- Chemical properties ,Heme -- Structure ,Heme -- Electric properties ,Myoglobin -- Chemical properties ,Myoglobin -- Structure ,Oxygen -- Chemical properties ,Substitution reactions -- Analysis ,Chemistry - Abstract
Strongly electron-withdrawing perfluoromethyl (C[F.sub.3]) groups are substituted as heme side chains of myoglobin (Mb) to obtain larger alterations of the heme electron structure in order to analyze the relationship between the [O.sub.2] affinity of Mb and the electronic properties of heme peripheral side chains. The introduction of electron-withdrawing groups has increased the preferential binding of CO to the protein over that of [O.sub.2].
- Published
- 2010
24. Role of a highly conserved electrostatic interaction on the surface of cytochrome c in control of the redox function
- Author
-
Hulin Tai, Mikami, Shin-ichi, Irie, Kiyofumi, Watanabe, Naoki, Shinohara, Naoya, and Yamamoto, Yasuhiko
- Subjects
Alanine -- Chemical properties ,Alanine -- Thermal properties ,Cytochrome c -- Chemical properties ,Electrostatic interactions -- Analysis ,Lysine -- Chemical properties ,Lysine -- Thermal properties ,Biological sciences ,Chemistry - Abstract
The functional consequences of removal of the electrostatic interaction through replacement of Lys8 by Ala are explored to better understand the molecular mechanisms responsible for functional control of the protein. The minute, but subtle, effects of removal of the conserved interaction on the thermodynamic properties of the protein demonstrated the significance of electrostatic interaction for maintaining the functional properties of the protein and the crucial role of amino acid residues relatively remote from the heme active site in the functional control of the protein.
- Published
- 2010
25. Photoactivation of the Ni-SIr state to the Ni-SIa state in [NiFe] hydrogenase: FT-IR study on the light reactivity of the ready Ni-SIr state and as-isolated enzyme revisited
- Author
-
Koji Nishikawa, Hulin Tai, Liyang Xu, Yoshiki Higuchi, Seiya Inoue, and Shun Hirota
- Subjects
chemistry.chemical_classification ,Hydrogenase ,biology ,Light ,010405 organic chemistry ,Chemistry ,Photochemistry ,General Physics and Astronomy ,010402 general chemistry ,biology.organism_classification ,01 natural sciences ,0104 chemical sciences ,Enzyme ,Light induced ,Reactivity (chemistry) ,Irradiation ,Desulfovibrio vulgaris ,Physical and Theoretical Chemistry ,Fourier transform infrared spectroscopy ,NiFe hydrogenase - Abstract
The Ni-SIr state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F was photoactivated to its Ni-SIa state by Ar(+) laser irradiation at 514.5 nm, whereas the Ni-SL state was light induced from a newly identified state, which was less active than any other identified state and existed in the "as-isolated" enzyme.
- Published
- 2016
26. Interaction between the Heme and a G-Quartet in a Heme–DNA Complex
- Author
-
Kaori Saito, Yasuhiko Yamamoto, Hikaru Hemmi, Nagao Kobayashi, and Hulin Tai
- Subjects
Models, Molecular ,Ligand field theory ,Circular dichroism ,Magnetic Resonance Spectroscopy ,Stereochemistry ,Iron ,Static Electricity ,Heme ,Ligands ,G-quadruplex ,Inorganic Chemistry ,chemistry.chemical_compound ,Static electricity ,Kinetic isotope effect ,Humans ,Physical and Theoretical Chemistry ,Repetitive Sequences, Nucleic Acid ,Circular Dichroism ,DNA ,Nuclear magnetic resonance spectroscopy ,G-Quadruplexes ,Oxygen ,chemistry ,Proton NMR ,Protons - Abstract
The structure of a complex between heme(Fe(3+)) and a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), has been characterized by (1)H NMR. The study demonstrated that the heme(Fe(3+)) is sandwiched between the 3'-terminal G-quartets of the G-quadruplex DNA. Hence, the net +1 charge of the heme(Fe(3+)) in the complex is surrounded by the eight carbonyl oxygen atoms of the G-quartets. Interaction between the heme Fe(3+) and G-quartets in the complex was clearly manifested in the solvent (1)H/(2)H isotope effect on the NMR parameters of paramagnetically shifted heme methyl proton signals, and interaction of the heme Fe(3+) with the eight carbonyl oxygen atoms of the two G-quartets was shown to provide a strong and axially symmetric ligand field surrounding the heme Fe(3+), yielding a heme(Fe(3+)) low-spin species with a highly symmetric heme electronic structure. This finding provides new insights as to the design of the molecular architecture and functional properties of various heme-DNA complexes.
- Published
- 2012
27. Fine tuning of the redox function of Pseudomonas aeruginosa cytochrome c551 through structural properties of a polypeptide loop bearing an axial Met residue
- Author
-
Yasuhiko Yamamoto, Shin-ichi Mikami, Tsuyoshi Udagawa, Hulin Tai, and Akihiro Sugimoto
- Subjects
Cytochrome ,biology ,Protein Conformation ,Protein Stability ,Chemistry ,Stereochemistry ,Hydrogen bond ,Mutant ,Cytochrome c Group ,Hydrogen Bonding ,Biochemistry ,Redox ,Inorganic Chemistry ,Residue (chemistry) ,chemistry.chemical_compound ,Bacterial Proteins ,Amide ,Pseudomonas aeruginosa ,Side chain ,biology.protein ,Peptides ,Oxidation-Reduction ,Heme - Abstract
Pseudomonas aeruginosa cytochrome c551 (PA) possesses a long polypeptide loop near its heme, and a unique hydrogen bond network among Ser52, axial Met61, and the heme 13-propionate side chain, i.e., Ser52 amide NH is hydrogen bonded to axial Met61 carbonyl CO, Met61 amide NH to Ser52 carbonyl CO, and Ser52 side chain OH to the heme 13-propionate side chain, contributes to stabilization of the structure of the loop [Y. Matsuura, T. Takano, R.E. Dickerson, J. Mol. Biol. 156 (1982) 389–409]. In this study, the structure and redox function of S52N and S52G mutants were characterized in order to elucidate the role of Ser52 in functional regulation of the protein. We found that the redox function of PA was hardly affected by an S52N mutation, but was slightly by an S52G one. The functional similarity between the wild-type protein and the S52N mutant demonstrated that Asn52 in the mutant plays a similar pivotal role in the formation of the unique hydrogen bond network that stabilizes the structure of the loop as Ser52 in the wild-type protein does. On the other hand, the functional alteration induced by the S52G mutation can be attributed to a structural change of the loop due to the lack of the hydrogen bond between the Gly52 and heme 13-propionate side chain in the mutant. Thus, this study demonstrated that the function of the protein can be tuned through the structural properties of the polypeptide loop near its heme.
- Published
- 2012
28. Structural characterization of a carbon monoxide adduct of a heme–DNA complex
- Author
-
Ryu Nishimura, Saburo Neya, Yasuhiko Yamamoto, Tomokazu Shibata, Masashi Fukaya, Hulin Tai, and Kaori Saito
- Subjects
Models, Molecular ,Carbon Monoxide ,Magnetic Resonance Spectroscopy ,Hemeprotein ,Molecular Structure ,biology ,Stereochemistry ,DNA ,Heme ,Nuclear magnetic resonance spectroscopy ,Biochemistry ,Porphyrin ,Cofactor ,Adduct ,G-Quadruplexes ,Inorganic Chemistry ,chemistry.chemical_compound ,chemistry ,biology.protein ,Humans ,Quantum Theory ,Molecule ,Organic chemistry ,Carbon monoxide - Abstract
The structure of a carbon monoxide (CO) adduct of a complex between heme and a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), has been characterized using ¹H and ¹³C NMR spectroscopy and density function theory calculations. The study revealed that the heme binds to the 3'-terminal G-quartet of the DNA though a π-π stacking interaction between the porphyrin moiety of the heme and the G-quartet. The π-π stacking interaction between the pseudo-C₂-symmetric heme and the C₄-symmetric G-quartet in the complex resulted in the formation of two isomers possessing heme orientations differing by 180° rotation about the pseudo-C₂ axis with respect to the DNA. These two slowly interconverting heme orientational isomers were formed in a ratio of approximately 1:1, reflecting that their thermodynamic stabilities are identical. Exogenous CO is coordinated to heme Fe on the side of the heme opposite the G-quartet in the complex, and the nature of the Fe-CO bond in the complex is similar to that of the Fe-CO bonds in hemoproteins. These findings provide novel insights for the design of novel DNA enzymes possessing metalloporphyrins as prosthetic groups.
- Published
- 2011
29. Characterization of the acid–alkaline transition in the individual subunits of human adult and foetal methaemoglobins
- Author
-
Tomokazu Shibata, Satoshi Nagao, Hiromi Hamada, Yasuhiko Yamamoto, Akihiro Suzuki, Hiroyuki Yoshikawa, Shigenori Nagatomo, and Hulin Tai
- Subjects
Adult ,Hemeprotein ,Chemistry ,digestive, oral, and skin physiology ,Allosteric regulation ,Prekallikrein ,Hemoglobin A ,Heme ,General Medicine ,Hydrogen-Ion Concentration ,Biochemistry ,Methemoglobin ,chemistry.chemical_compound ,Myoglobin ,Fetal hemoglobin ,Side chain ,Humans ,Thermodynamics ,Spectrophotometry, Ultraviolet ,Nuclear Magnetic Resonance, Biomolecular ,Molecular Biology ,Fetal Hemoglobin - Abstract
Human adult haemoglobin (Hb A), a tetrameric oxygen transfer haemoprotein, has been recognized as an excellent model for investigating the structure-function relationships in allosteric proteins, and has been characterized exhaustively from both experimental and theoretical aspects. Despite the detailed structural and spectroscopic information available for the protein, functional properties have not been as fully elucidated as expected, and hence have remained unexplored. A major drawback for the functional characterization of Hb A is the lack of experimental techniques which enable quantitative characterization of functional properties of the individual subunits of the intact protein. In this study, we have developed techniques for determining the equilibrium constant of the acid-alkaline transition, usually represented as the 'pK(a)' value, in the individual subunits of the met-forms of Hb A (metHb A) and human foetal haemoglobin (metHb F). The pK(a) values of the individual subunits of metHb A and metHb F have been shown to constitute novel and highly sensitive probes for characterizing the effects of structural changes of not only the interfaces between the subunits within the protein, but also the contact between haem and the protein in the haem pocket. In addition, haem replacement studies of the proteins revealed that the contact between the haem peripheral vinyl side chain and the protein in the haem pocket is important for maintaining the non-equivalence in the haem environment between the subunits of Hb A and Hb F, which could be relevant to the cooperative ligand binding of the proteins.
- Published
- 2010
30. Role of a Highly Conserved Electrostatic Interaction on the Surface of Cytochrome c in Control of the Redox Function
- Author
-
Naoki Watanabe, Shin-ichi Mikami, Kiyofumi Irie, Yasuhiko Yamamoto, Hulin Tai, and Naoya Shinohara
- Subjects
Models, Molecular ,Cytochrome ,Protein Conformation ,Static Electricity ,medicine.disease_cause ,Biochemistry ,Redox ,Structure-Activity Relationship ,Protein structure ,Bacterial Proteins ,medicine ,Denaturation (biochemistry) ,Mutation ,Bacteria ,biology ,Chemistry ,Circular Dichroism ,Hydrogenobacter thermophilus ,Cytochrome c ,Cytochromes c ,biology.organism_classification ,Crystallography ,Intramolecular force ,Biophysics ,biology.protein ,Thermodynamics ,Oxidation-Reduction - Abstract
In Hydrogenobacter thermophilus cytochrome c(552), an electrostatic interaction between Lys8 and Glu68 in the N- and C-terminal helices, respectively, stabilizes its protein structure [Travaglini-Allocatelli, C., Gianni, S., Dubey, V. K., Borgia, A., Di Matteo, A., Bonivento, D., Cutruzzola, F., Bren, K. L., and Brunori, M. (2005) J. Biol. Chem. 280, 25729-25734], this electrostatic interaction being a highly conserved structural feature of the cytochrome c family. In the present study, the functional consequences of removal of the interaction through replacement of Lys8 by Ala have been investigated in order to elucidate the molecular mechanisms responsible for functional control of the protein. The mutation resulted in a decrease in protein stability, as reflected in lowering of the denaturation temperature by approximately 2-9 degrees C, and a negative shift by approximately 8 mV of the redox potential (E(m)) of the protein. The decrease in the protein stability was attributed to the enthalpic loss due to the removal of the intramolecular interaction. The negative shift of the E(m) value was shown to be due to the effect of the mutation on the entropic contribution to the E(m) value. The small, but subtle, effects of removal of the conserved electrostatic interaction, occurring at approximately 1.4 nm away from heme iron, on the thermodynamic properties of the protein demonstrated not only that the interaction is important for maintaining the functional properties of the protein but also that amino acid residues relatively remote from the heme active site play sizable roles in functional control of the protein.
- Published
- 2009
31. Effect of the Redox-Dependent Ionization State of the Heme Propionic Acid Side Chain on the Entropic Contribution to the Redox Potential of Pseudomonas aeruginosa Cytochrome c551
- Author
-
Hulin Tai, Yasuhiko Yamamoto, and Shin-ichi Mikami
- Subjects
Cytochrome ,Stereochemistry ,Entropy ,Mutant ,Cytochrome c Group ,Heme ,medicine.disease_cause ,Biochemistry ,Redox ,Structure-Activity Relationship ,chemistry.chemical_compound ,Bacterial Proteins ,Oxidation state ,Cations ,Ionization ,Electrochemistry ,medicine ,Side chain ,Bacteria ,biology ,Pseudomonas aeruginosa ,Chemistry ,Hydrogen Bonding ,Hydrogen-Ion Concentration ,biology.protein ,Propionates ,Oxidation-Reduction - Abstract
The thermodynamic properties of the redox potentials (E(m)) of Pseudomonas aeruginosa cytochrome c(551) (PA) and its mutants possessing a variety of pK(a) values for the heme 17-propionic acid side chain, which ranged from approximately 5 to approximately 8, have been investigated to elucidate the role of ionization of the heme side chain in the E(m) control. Since the pK(a) values of the heme 17-propionic acid side chains of the oxidized and reduced forms of PA are 5.9 +/- 0.2 and 7.0 +/- 0.2, respectively [Takayama, S. J., Mikami, S., Terui, N., Mita, H., Hasegawa, J., Sambongi, Y., and Yamamoto, Y. (2005) Biochemistry 44, 5488-5494], the ionization state of the heme 17-propionic acid side chain at physiological pH depends on the oxidation state of the protein. This redox-dependent ionization state of the heme 17-propionic acid side chain was found to have a large effect on the entropic contribution (DeltaS) to the E(m) value. The magnitude of the E(m) control through the DeltaS value due to the redox-dependent ionization state of the heme 17-propionic acid side chain was shown to be about 170 mV and hence is considerably larger than that through the enthalpic contribution (DeltaH) to the E(m) value due to stabilization of the cationic ferriheme in the oxidized protein through partial neutralization of its positive charge by the heme 17-propionate side chain, i.e., about 60 mV [Takayama, S. J., Mikami, S., Terui, N., Mita, H., Hasegawa, J., Sambongi, Y., and Yamamoto, Y. (2005) Biochemistry 44, 5488-5494]. The present study revealed that the heme 17-propionic acid side chain of the protein plays a pivotal role in the E(m) control of the protein.
- Published
- 2009
32. Electron transfer from cytochrome c to cupredoxins
- Author
-
Shin-ichi J. Takayama, Antonio Donaire, Kiyofumi Irie, Yasuhiko Yamamoto, Luis A. Alcaraz, Takumi Kawahara, Teruhiro Takabe, Hulin Tai, and Shun Hirota
- Subjects
Models, Molecular ,Cytochrome ,Protein Conformation ,Stereochemistry ,Biochemistry ,Electron Transport ,Inorganic Chemistry ,Electron transfer ,Azurin ,Rusticyanin ,Aquifoliaceae ,Plastocyanin ,biology ,Chemistry ,Cytochrome c ,Cytochromes c ,Hydrogen-Ion Concentration ,Electron transport chain ,Marcus theory ,Kinetics ,Pseudomonas aeruginosa ,biology.protein ,Thermodynamics ,Hydrophobic and Hydrophilic Interactions - Abstract
Electron transfer (ET) through and between proteins is a fundamental biological process. The activation energy for an ET reaction depends upon the Gibbs energy change upon ET (DeltaG(0)) and the reorganization energy. Here, we characterized ET from Pseudomonas aeruginosa cytochrome c(551) (PA) and its designed mutants to cupredoxins, Silene pratensis plastocyanin (PC) and Acidithiobacillus ferrooxidans rusticyanin (RC), through measurement of pseudo-first-order ET rate constants (k(obs)). The influence of the DeltaG (0) value for ET from PA to PC or RC on the k(obs) value was examined using a series of designed PA proteins exhibiting a variety of E (m) values, which afford the DeltaG (0) variation range of 58-399 meV. The plots of the k(obs) values obtained against the DeltaG(0) values for both PA-PC and PA-RC redox pairs could be fitted well with a single Marcus equation. We have shown that the ET activity of cytochrome c can be controlled by tuning the E(m) value of the protein through the substitution of amino acid residues located in hydrophobic-core regions relatively far from the redox center. These findings provide novel insights into the molecular design of cytochrome c, which could be utilized for controlling its ET activity by means of protein engineering.
- Published
- 2009
33. Stability of the Heme Fe−N-Terminal Amino Group Coordination Bond in Denatured Cytochrome c
- Author
-
Toratane Munegumi, Yasuhiko Yamamoto, and Hulin Tai
- Subjects
Protein Denaturation ,Magnetic Resonance Spectroscopy ,Nitrogen ,Stereochemistry ,Iron ,Electrons ,Heme ,Inorganic Chemistry ,chemistry.chemical_compound ,Residue (chemistry) ,Aquifoliaceae ,Histidine ,Amino Acid Sequence ,Physical and Theoretical Chemistry ,Guanidine ,Peptide sequence ,biology ,Hydrogenobacter thermophilus ,Cytochrome c ,Cytochromes c ,Nuclear magnetic resonance spectroscopy ,biology.organism_classification ,chemistry ,Mutation ,Pseudomonas aeruginosa ,biology.protein ,Oxidation-Reduction - Abstract
In the denatured states of Hydrogenobacter thermophilus cytochrome c(552) (HT) and Pseudomonas aeruginosa cytochrome c(551) (PA), and their mutants, the N-terminal amino group of the polypeptide chain is coordinated to heme Fe in place of the axial Met, the His-N(term) form being formed. The coordination of the N-terminal amino group to heme Fe leads to loop formation by the N-terminal stretch preceding the first Cys residue bound to the heme, and the N-terminal stretches of HT and PA are different from each other in terms of both the sequence and the number of constituent amino acid residues. The His-N(term) form was shown to be rather stable, and hence it can influence the stability of the denatured state. We have investigated the heme Fe coordination structures and stabilities of the His-N(term) forms emerging upon guanidine hydrochloric acid-induced unfolding of the oxidized forms of the proteins. The Fe-N(term) coordination bond in the His-N(term) form with a 9-residue N-terminal stretch of HT proteins was found to be tilted to some extent away from the heme normal, as reflected by the great heme methyl proton shift spread. On the other hand, the small heme methyl proton shift spread of the His-N(term) form with an 11-residue stretch of PA proteins indicated that its Fe-N(term) bond is nearly parallel with the heme normal. The stability of the His-N(term) form was found to be affected by the structural properties of the N-terminal stretch, such as its length and the N-terminal residue. With a given N-terminal residue, the stability of the His-N(term) form is higher for a 9-residue N-terminal stretch than an 11-residue one. In addition, with a given length of the N-terminal stretch, the His-N(term) form with an N-terminal Glu is stabilized by a few kJ mol(-1) relative to that with an N-terminal Asn. These results provide a novel insight into the stabilizing interactions in the denatured cyts c that will facilitate elucidation of the folding/unfolding mechanisms of the proteins.
- Published
- 2008
34. Characterization of N-terminal amino group–heme ligation emerging upon guanidine hydrochloric acid induced unfolding of Hydrogenobacter thermophilus ferricytochrome c 552
- Author
-
Yasuhiko Yamamoto, Shin Kawano, and Hulin Tai
- Subjects
Protein Denaturation ,Circular dichroism ,Cytochrome ,Peptide ,Heme ,Biochemistry ,Inorganic Chemistry ,chemistry.chemical_compound ,Guanidine ,Nuclear Magnetic Resonance, Biomolecular ,chemistry.chemical_classification ,Bacteria ,biology ,Circular Dichroism ,Cytochrome c ,Hydrogenobacter thermophilus ,Cytochromes c ,Hydrogen-Ion Concentration ,biology.organism_classification ,Crystallography ,chemistry ,biology.protein ,Spectrophotometry, Ultraviolet ,Protein folding ,Acids - Abstract
Nonnative heme coordination structures emerging upon guanidine hydrochloric acid (GdnHCl) induced unfolding of Hydrogenobacter thermophilus ferricytochrome c552 were characterized by means of paramagnetic NMR. The heme coordination structure possessing the N-terminal amino group of the peptide chain in place of axial Met (His-Nterm form) was determined in the presence of GdnHCl concentrations in excess of 1.5 M at neutral pH. The stability of the His-Nterm form at pH 7.0 was found to be comparable with that of the bis-His form which has been recognized as a major nonnative heme coordination structure in cytochrome c folding/unfolding. Consequently, in addition to the bis-His form, the His-Nterm form is a substantial intermediate which affects the pathway and kinetics of the folding/unfolding of cytochromes c, of which the N-terminal amino groups are not acetylated.
- Published
- 2007
35. ChemInform Abstract: Characterization of the Interaction Between Heme and a Parallel G-Quadruplex DNA Formed from d(TTAGGGT)
- Author
-
Haruna Shimizu, Masashi Kinoshita, Yasuhiko Yamamoto, Tomokazu Shibata, Kaori Saito, and Hulin Tai
- Subjects
chemistry.chemical_compound ,chemistry ,Biochemistry ,Stereochemistry ,Nucleic acid ,Molecule ,heterocyclic compounds ,General Medicine ,Electronic structure ,G-quadruplex ,Heme ,DNA ,Characterization (materials science) - Abstract
The molecular structure and heme electronic structure of a complex (heme–(d(TTAGGGT))4 complex) between heme and a parallel G-quadruplex DNA formed from heptanucleotide d(TTAGGGT), i.e., (d(TTAGGGT...
- Published
- 2015
36. Characterization of Non-Native Heme Coordination Structures Emerging upon Guanidine Hydrochloric Acid-Induced Unfolding ofPseudomonas aeruginosaFerricytochromec551
- Author
-
Hulin Tai, Yoshihiro Sambongi, Yasuhiko Yamamoto, Hajime Mita, and Shigenori Nagatomo
- Subjects
Circular dichroism ,biology ,Cytochrome ,Stereochemistry ,Ligand ,Resonance Raman spectroscopy ,Active site ,General Chemistry ,Cleavage (embryo) ,chemistry.chemical_compound ,Crystallography ,chemistry ,biology.protein ,Guanidine ,Heme - Abstract
The non-native heme coordination structures emerging upon guanidine hydrochloric acid (GdnHCl)-induced unfolding of Pseudomonas aeruginosa ferricytochrome c 5 5 1 were characterized by absorption, circular dichroism, paramagnetic NMR, and resonance Raman spectroscopy. Hexacoordinated high-spin ferriheme bearing axial His and H 2 O ligands, and pentacoordinated high-spin ferriheme with an axial His ligand were identified in the presence of GdnHCl concentrations ≥ 1.5 M (M = mol dm - 3 ). These non-native species were rapidly interconverted to each other through cleavage/formation of the Fe-H 2 O coordination bond, and were also in dynamic equilibrium, at a rate of < 2 × 10 4 s - 1 , with the native species. Thus, the present study demonstrated the presence of dynamic equilibrium through cleavage/formation of a Fe-H 2 O coordination bond in an unfolding intermediate. These results provide a deeper insight into structure transitions of the heme active site upon folding and unfolding of cytochrome c.
- Published
- 2005
37. Electronic control of ligand-binding preference of a myoglobin mutant
- Author
-
Saburo Neya, Takashi Matsuo, Sachiko Yanagisawa, Akihiro Suzuki, Shun Hirota, Takashi Ogura, Tomokazu Shibata, Hulin Tai, Ryu Nishimura, Daichi Matsumoto, and Yasuhiko Yamamoto
- Subjects
biology ,Chemistry ,Stereochemistry ,Hydrogen bond ,Myoglobin ,Proton Magnetic Resonance Spectroscopy ,Mutant ,Phenylalanine ,Ligands ,Cofactor ,Inorganic Chemistry ,chemistry.chemical_compound ,Mutant protein ,Mutation ,biology.protein ,Organic chemistry ,Physical and Theoretical Chemistry ,Heme ,Carbon monoxide - Abstract
The L29F mutant of sperm whale myoglobin (Mb), where the leucine 29 residue was replaced by phenylalanine (Phe), was shown to exhibit remarkably high affinity to oxygen (O2), possibly due to stabilization of the heme Fe atom-bound O2 in the mutant protein through a proposed unique electrostatic interaction with the introduced Phe29, in addition to well-known hydrogen bonding with His64 [Carver, T. E.; Brantley, R. E.; Singleton, E. W.; Arduini, R. M.; Quillin, M. L.; Phillips, G. N., Jr.; Olson, J. S. J. Biol. Chem., 1992, 267, 14443-14450]. We analyzed the O2 and carbon monoxide (CO) binding properties of the L29F mutant protein reconstituted with chemically modified heme cofactors possessing a heme Fe atom with various electron densities, to determine the effect of a change in the electron density of the heme Fe atom (ρ(Fe)) on the O2 versus CO discrimination. The study demonstrated that the preferential binding of O2 over CO by the protein was achieved through increasing ρ(Fe), and the ordinary ligand-binding preference, that is, the preferential binding of CO over O2, by the protein was achieved through decreasing ρ(Fe). Thus, the O2 and CO binding preferences of the L29F mutant protein could be controlled through electronic modulation of intrinsic heme Fe reactivity through a change in ρ(Fe). The present study highlighted the significance of the tuning of the intrinsic heme Fe reactivity through the heme electronic structure in functional regulation of Mb.
- Published
- 2014
38. Inversion of the stereochemistry around the sulfur atom of the axial methionine side chain through alteration of amino acid side chain packing in Hydrogenobacter thermophilus cytochrome C552 and its functional consequences
- Author
-
Nagao Kobayashi, Ken Tonegawa, Hulin Tai, Yasuhiko Yamamoto, Tomokazu Shibata, and Hikaru Hemmi
- Subjects
Models, Molecular ,Cytochrome ,Stereochemistry ,Molecular Sequence Data ,Cytochrome c Group ,Biochemistry ,chemistry.chemical_compound ,Residue (chemistry) ,Methionine ,Enzyme Stability ,Side chain ,Amino Acid Sequence ,Amino Acids ,Lone pair ,Heme ,Nuclear Magnetic Resonance, Biomolecular ,biology ,Bacteria ,Chemistry ,Hydrogenobacter thermophilus ,Cytochrome c ,Circular Dichroism ,Temperature ,Stereoisomerism ,biology.organism_classification ,Mutation ,biology.protein ,Sulfur - Abstract
In cytochrome c, the coordination of the axial Met Sδ atom to the heme Fe atom occurs in one of two distinctly different stereochemical manners, i.e., R and S configurations, depending upon which of the two lone pairs of the Sδ atom is involved in the bond; hence, the Fe-coordinated Sδ atom becomes a chiral center. In this study, we demonstrated that an alteration of amino acid side chain packing induced by the mutation of a single amino acid residue, i.e., the A73V mutation, in Hydrogenobacter thermophilus cytochrome c552 (HT) forces the inversion of the stereochemistry around the Sδ atom from the R configuration [Travaglini-Allocatelli, C., et al. (2005) J. Biol. Chem. 280, 25729-25734] to the S configuration. Functional comparison between the wild-type HT and the A73V mutant possessing the R and S configurations as to the stereochemistry around the Sδ atom, respectively, demonstrated that the redox potential (Em) of the mutant at pH 6.00 and 25 °C exhibited a positive shift of ∼20 mV relative to that of the wild-type HT, i.e., 245 mV, in an entropic manner. Because these two proteins have similar enthalpically stabilizing interactions, the difference in the entropic contribution to the Em value between them is likely to be due to the effect of the conformational alteration of the axial Met side chain associated with the inversion of the stereochemistry around the Sδ atom due to the effect of mutation on the internal mobility of the loop bearing the axial Met. Thus, the present study demonstrated that the internal mobility of the loop bearing the axial Met, relevant to entropic control of the redox function of the protein, is affected quite sensitively by the contextual stereochemical packing of amino acid side chains in the proximity of the axial Met.
- Published
- 2013
39. Relationship between oxygen affinity and autoxidation of myoglobin
- Author
-
Kiyohiro Imai, Tomokazu Shibata, Ryu Nishimura, Satoshi Nagao, Yasuhiko Yamamoto, Ariki Matsuoka, Daichi Matsumoto, Akihiro Suzuki, Shun Hirota, Saburo Neya, Takashi Matsuo, and Hulin Tai
- Subjects
Electron density ,Autoxidation ,biology ,Chemistry ,Ligand ,Myoglobin ,Whales ,Heme ,Resonance (chemistry) ,Ligands ,Cofactor ,Inorganic Chemistry ,Reaction rate ,Oxygen ,chemistry.chemical_compound ,Crystallography ,Kinetics ,biology.protein ,Animals ,Spectrophotometry, Ultraviolet ,Physical and Theoretical Chemistry ,Oxidation-Reduction - Abstract
Studies using myoglobins reconstituted with a variety of chemically modified heme cofactors revealed that the oxygen affinity and autoxidation reaction rate of the proteins are highly correlated to each other, both decreasing with decreasing the electron density of the heme iron atom. An Fe(3+)-O(2)(-)-like species has been expected for the Fe(2+)-O(2) bond in the protein, and the electron density of the heme iron atom influences the resonance process between the two forms. A shift of the resonance toward the Fe(2+)-O(2) form results in lowering of the O(2) affinity due to an increase in the O(2) dissociation rate. On the other hand, a shift of the resonance toward the Fe(3+)-O(2)(-)-like species results in acceleration of the autoxidation through increasing H(+) affinity of the bound ligand.
- Published
- 2012
40. Enhancement of the thermostability of Hydrogenobacter thermophilus cytochrome c(552) through introduction of an extra methylene group into its hydrophobic protein interior
- Author
-
Kiyofumi Irie, Shin-ichi Mikami, Hulin Tai, and Yasuhiko Yamamoto
- Subjects
Models, Molecular ,Cytochrome ,Stereochemistry ,Cytochrome c Group ,medicine.disease_cause ,Protein Engineering ,Biochemistry ,chemistry.chemical_compound ,Catalytic Domain ,Enzyme Stability ,medicine ,Aquifoliaceae ,Transition Temperature ,Methylene ,Heme ,Thermostability ,Mutation ,biology ,Chemistry ,Hydrogenobacter thermophilus ,Temperature ,Hydrogen-Ion Concentration ,biology.organism_classification ,Amino Acid Substitution ,Void space ,biology.protein ,Hydrophobic and Hydrophilic Interactions ,Methyl group - Abstract
Careful scrutiny of the protein interior of Hydrogenobacter thermophilus cytochrome c(552) (HT) on the basis of its X-ray structure [Travaglini-Allocatelli, C., Gianni, S., Dubey, V. K., Borgia, A., Di Matteo, A., Bonivento, D., Cutruzzola, F., Bren, K. L., and Brunori, M. (2005) J. Biol. Chem. 280, 25729-25734] indicated that a void space, which is large enough to accommodate a methyl group, exists in the hydrophobic protein interior near the heme. We tried to reduce the void space through the replacement of a Val by Ile or Leu (Val/Ile or Val/Leu mutation), and then the structural and functional consequences of these two mutations were characterized in order to elucidate the relationship between the nature of the packing of hydrophobic residues and the functional properties of the protein. The study demonstrated striking differences in the structural and functional consequences between the two mutations. The Val/Ile mutation was found to cause further enhancement of the thermostability of the oxidized HT, as reflected in the increase of the denaturation temperature (T(m)) value by ∼ 3 deg, whereas the thermostability of the reduced form was essentially unaffected. As a result, the redox potential (E(m)) of the Val/Ile mutant exhibited a negative shift of ∼ 50 mV relative to that of the wild-type protein in an enthalpic manner, this being consistent with our previous finding that a protein with higher stability in its oxidized form exhibits a lower E(m) value [Terui, N., Tachiiri, N., Matsuo, H., Hasegawa, J., Uchiyama, S., Kobayashi, Y., Igarashi, Y., Sambongi, Y., and Yamamoto, Y. (2003) J. Am. Chem. Soc. 125, 13650-13651]. In contrast, the Val/Leu mutation led to a decrease in thermostability of both the redox forms of the protein, as reflected in the decreases of the T(m) values of the oxidized and reduced proteins by ∼ 3 and ∼ 5 deg, respectively, and the E(m) value of the Val/Leu mutant happened to be similar to that of the Val/Ile one. The E(m) value of the Val/Leu mutant could be reasonably interpreted in terms of the different effects of the mutation on the stabilities of the two different redox forms of the protein. Thus, the present study demonstrated that the stability of the protein is affected quite sensitively by the contextual stereochemical packing of hydrophobic residues in the protein interior and that the structural properties of the hydrophobic core in the protein interior are crucial for control of the redox function of the protein. These findings provide novel insights as to functional control of a protein, which could be utilized for tuning of the T(m) and E(m) values of the protein by means of protein engineering.
- Published
- 2011
41. Control of the stability of Hydrogenobacter thermophilus cytochrome C(552) through alteration of the basicity of the N-terminal amino group of the polypeptide chain
- Author
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Yasuhiko Yamamoto, Toratane Munegumi, and Hulin Tai
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Protein Denaturation ,Cytochrome ,Stereochemistry ,Cytochrome c Group ,Inorganic Chemistry ,chemistry.chemical_compound ,Residue (chemistry) ,Enzyme Stability ,Point Mutation ,Histidine ,Physical and Theoretical Chemistry ,Heme ,Nuclear Magnetic Resonance, Biomolecular ,biology ,Bacteria ,Chemistry ,Hydrogenobacter thermophilus ,Cytochrome c ,Hydrogen-Ion Concentration ,biology.organism_classification ,Folding (chemistry) ,Amino Acid Substitution ,biology.protein ,Thermodynamics ,Chemical stability ,Mutant Proteins - Abstract
In the denatured state of Hydrogenobacter thermophilus cytochrome c(552) (HT), the N-terminal amino group of the polypeptide chain is coordinated to the heme Fe in place of the axial Met, the His-N(term) form being formed [Tai, H., Munegumi, T., Yamamoto, Y. Inorg. Chem. 2009, 48, 331-338]. Since the His-N(term) form can be considered as an ordered residual structure in the denatured protein, its stability significantly influences the energy of the denatured state. In this study, the His-N(term) forms of the wild-type HT and its mutants possessing a series of amino acid residues at the N-terminal, such as N1D, N1E, and N1G, have been characterized to elucidate the physicochemical properties of the N-terminal residue responsible for the control of the thermodynamic stability of the His-N(term) form. The study revealed that the thermodynamic stability of the His-N(term) form depends highly on the basicity of the N-terminal amino group of the polypeptide chain in such a manner that an increase in the pK(a) value of the N-terminal amino group by 1 unit results in stabilization of the bond between heme Fe and the N-terminal amino group (Fe-N(term) bond) in the His-N(term) form by ∼4 kJ mol(-1). The empirical hard and soft acid and base principle could account for the observed relationship between the pK(a) value of the N-terminal amino group and the stability of the Fe-N(term) bond in the His-N(term) form. In addition, the study demonstrated that the overall stability of the protein can be manipulated through the energy of the denatured protein by changing the thermodynamic stability of the His-N(term) form. Consequently, the overall stability of the protein has been shown to be controlled through alteration of the basicity of the N-terminal amino group of the polypeptide chain. These findings provide new insights into the stabilizing interactions in the denatured protein, which are relevant as to characterization of the protein stability and folding.
- Published
- 2010
42. Effect of heme modification on oxygen affinity of myoglobin and equilibrium of the acid-alkaline transition in metmyoglobin
- Author
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Tomokazu Shibata, Shigenori Nagatomo, Shun Hirota, Satoshi Nagao, Masashi Fukaya, Kenji Morihashi, Yasuhiko Yamamoto, Akihiro Suzuki, Kiyohiro Imai, Takashi Matsuo, and Hulin Tai
- Subjects
Electrons ,Electronic structure ,Heme ,Alkalies ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Side chain ,Organic chemistry ,Reactivity (chemistry) ,Nuclear Magnetic Resonance, Biomolecular ,Equilibrium constant ,Carbon Monoxide ,Myoglobin ,General Chemistry ,Hydrogen-Ion Concentration ,Oxygen ,Crystallography ,chemistry ,Metmyoglobin ,Density functional theory ,Acids - Abstract
Functional regulation of myoglobin (Mb) is thought to be achieved through the heme environment furnished by nearby amino acid residues, and subtle tuning of the intrinsic heme Fe reactivity. We have performed substitution of strongly electron-withdrawing perfluoromethyl (CF(3)) group(s) as heme side chain(s) of Mb to obtain large alterations of the heme electronic structure in order to elucidate the relationship between the O(2) affinity of Mb and the electronic properties of heme peripheral side chains. We have utilized the equilibrium constant (pK(a)) of the "acid-alkaline transition" in metmyoglobin in order to quantitatively assess the effects of the CF(3) substitutions for the electron density of heme Fe atom (rho(Fe)) of the protein. The pK(a) value of the protein was found to decrease by approximately 1 pH unit upon the introduction of one CF(3) group, and the decrease in the pK(a) value with decreasing the rho(Fe) value was confirmed by density functional theory calculations on some model compounds. The O(2) affinity of Mb was found to correlate well with the pK(a) value in such a manner that the P(50) value, which is the partial pressure of O(2) required to achieve 50% oxygenation, increases by a factor of 2.7 with a decrease of 1 pK(a) unit. Kinetic studies on the proteins revealed that the decrease in O(2) affinity upon the introduction of an electron-withdrawing CF(3) group is due to an increase in the O(2) dissociation rate. Since the introduction of a CF(3) group substitution is thought to prevent further Fe(2+)-O(2) bond polarization and hence formation of a putative Fe(3+)-O(2)(-)-like species of the oxy form of the protein [Maxwell, J. C.; Volpe, J. A.; Barlow, C. H.; Caughey, W. S. Biochem. Biophys. Res. Commun. 1974, 58, 166-171], the O(2) dissociation is expected to be enhanced by the substitution of electron-withdrawing groups as heme side chains. We also found that, in sharp contrast to the case of the O(2) binding to the protein, the CO association and dissociation rates are essentially independent of the rho(Fe) value. As a result, the introduction of electron-withdrawing group(s) enhances the preferential binding of CO to the protein over that of O(2). These findings not only resolve the long-standing issue of the mechanism underlying the subtle tuning of the intrinsic heme Fe reactivity, but also provide new insights into the structure-function relationship of the protein.
- Published
- 2010
43. Activation Mechanism of the Streptomyces Tyrosinase Assisted by the Caddie Protein.
- Author
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Yasuyuki Matoba, Shogo Kihara, Yoshimi Muraki, Naohiko Bando, Hironari Yoshitsu, Teruo Kuroda, Miyuki Sakaguchi, Kure'e Kayama, Hulin Tai, Shun Hirota, Takashi Ogura, and Masanori Sugiyama
- Published
- 2017
- Full Text
- View/download PDF
44. 3P096 Preparation of myoglobin mutants exhibiting preferential binding of oxygen over carbon monoxide(02. Heme proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))
- Author
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Sachiko Yanagisawa, Daichi Matsumoto, Takashi Ogura, Tomokazu Shibata, Shun Hirota, Ryu Nishimura, Yasuhiko Yamamoto, Hulin Tai, Akihiro Suzuki, Saburo Neya, and Takashi Matsuo
- Subjects
chemistry.chemical_compound ,Hemeprotein ,Myoglobin ,chemistry ,Biochemistry ,Mutant ,chemistry.chemical_element ,Preferential binding ,Oxygen ,Carbon monoxide - Published
- 2014
45. Characterization of heme coordination structure in heme-DNA complex possessing gaseous molecule as an exogenous ligand
- Author
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Kaori Saito, Hikaru Hemmi, Shigenori Nagatomo, Hulin Tai, Hajime Mita, Yasuhiko Yamamoto, and Yusuke Nakano
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chemistry.chemical_classification ,Carbon Monoxide ,Hemeprotein ,Stereochemistry ,Ligand ,Spectrum Analysis ,Protoporphyrins ,DNA ,Heme ,General Medicine ,Ligands ,Photochemistry ,Coordination complex ,G-Quadruplexes ,Oxygen ,chemistry.chemical_compound ,chemistry ,Myoglobin ,Molecule ,Gases ,Hemeproteins ,Nuclear Magnetic Resonance, Biomolecular - Abstract
We have previously demonstrated that heme, iron(III)-protoporphyrin IX complex, and a parallel-quadruplex DNA assembled from d(TTAGGG) form a stable coordination complex called "heme-DNA complex". The heme-DNA complex exhibits a variety of spectroscopic characteristics remarkably similar to those of met-form of myoglobin, oxygen-binding hemoprotein, reflecting that the heme environments in the two systems are highly alike to each other. In a course of our effort toward exploring functional properties of the heme-DNA complex, we have investigated binding of gaseous molecules such as CO and O(2) to the heme-DNA complex. The present study revealed that the heme-DNA complex exhibits ability to accommodate these molecules as exogenous ligands.
- Published
- 2009
46. Characterization of Heme-DNA Complexes Composed of Some Chemically Modified Hemes and Parallel G-Quadruplex DNAs.
- Author
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Yasuhiko Yamamoto, Masashi Kinoshita, Yuya Katahira, Haruna Shimizu, Yue Di, Tomokazu Shibata, Hulin Tai, Akihiro Suzuki, and Saburo Neya
- Published
- 2015
- Full Text
- View/download PDF
47. FT-IR Characterization of the Light-Induced Ni-L2and Ni-L3 States of [NiFe] Hydrogenase from DesulfovibriovulgarisMiyazaki F.
- Author
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Hulin Tai, Koji Nishikawa, Seiya Inoue, Yoshiki Higuchi, and Shun Hirota
- Subjects
- *
HYDROGENASE , *IRON-nickel alloys , *FOURIER transform infrared spectroscopy , *CATALYTIC activity , *PROTON transfer reactions - Abstract
Different light-induced Ni-L statesof [NiFe] hydrogenase fromits Ni-C state have previously been observed by EPR spectroscopy.Herein, we succeeded in detecting simultaneously two Ni-L states of[NiFe] hydrogenase from Desulfovibrio vulgarisMiyazaki F by FT-IR spectroscopy. A new light-induced νCOband at 1890 cm–1and νCNbands at 2034 and 2047 cm–1were detected in theFT-IR spectra of the H2-activated enzyme under N2atmosphere at basic conditions, in addition to the 1910 cm–1νCOband and 2047 and 2061 cm–1νCNbands of the Ni-L2 state. The new bands wereattributed to the Ni-L3 state by comparison of the FT-IR and EPR spectra.The νCOand νCNfrequencies of theNi-L3 state are the lowest frequencies observed among the correspondingfrequencies of standard-type [NiFe] hydrogenases in various redoxstates. These results indicate that a residue, presumably Ni-coordinatingCys546, is protonated and deprotonated in the Ni-L2 and Ni-L3 states,respectively. Relatively small ΔH(6.4 ±0.8 kJ mol–1) and ΔS(25.5± 10.3 J mol–1K–1) valueswere obtained for the conversion from the Ni-L2 to Ni-L3 state, whichwas in agreement with the previous proposals that deprotonation ofCys546 is important for the catalytic reaction of the enzyme. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
48. Electronic Control of Ligand-Binding Preference of a Myoglobin Mutant.
- Author
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Ryu Nishimura, Daichi Matsumoto, Tomokazu Shibata, Sachiko Yanagisawa, Takashi Ogura, Hulin Tai, Takashi Matsuo, Shun Hirota, Saburo Neya, Akihiro Suzuki, and Yasuhiko Yamamoto
- Published
- 2014
- Full Text
- View/download PDF
49. Electronic Control of Discrimination between O22 and CO in Myoglobin Lacking the Distal Histidine Residue.
- Author
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Ryu Nishimura, Tomokazu Shibata, Izumi Ishigami, Takashi Ogura, Hulin Tai, Satoshi Nagao, Takashi Matsuo, Shun Hirota, Osami Shoji, Yoshihito Watanabe, Kiyohiro Imai, Saburo Neya, Akihiro Suzuki, and Yasuhiko Yamamoto
- Published
- 2014
- Full Text
- View/download PDF
50. Inversion of the Stereochemistry around the Sulfur Atom of the Axial Methionine Side Chain through Alteration of Amino Acid Side Chain Packing in Hydrogenobacter thermophilus Cytochrome c552 and Its Functional Consequences.
- Author
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Hulin Tai, Tonegawa, Ken, Shibata, Tomokazu, Hemmi, Hikaru, Kobayashi, Nagao, and Yamamoto, Yasuhiko
- Subjects
- *
STEREOCHEMISTRY , *SULFUR analysis , *METHIONINE , *SUBSTITUENTS (Chemistry) , *CYTOCHROME c , *MOLECULAR structure of amino acids - Abstract
In cytochrome c, the coordination of the axial Met Sδ atom to the heme Fe atom occurs in one of two distinctly different stereochemical manners, i.e., R and S configurations, depending upon which of the two lone pairs of the Sd atom is involved in the bond; hence, the Fe-coordinated Sd atom becomes a chiral center. In this study, we demonstrated that an alteration of amino acid side chain packing induced by the mutation of a single amino acid residue, i.e., the A73V mutation, in Hydrogenobacter thermophilus cytochrome c552 (HT) forces the inversion of the stereochemistry around the Sd atom from the R configuration [Travaglini-Allocatelli, C., et al. (2005) J. Biol. Chem. 280, 25729-25734] to the S configuration. Functional comparison between the wild-type HT and the A73V mutant possessing the R and S configurations as to the stereochemistry around the Sd atom, respectively, demonstrated that the redox potential (Em) of the mutant at pH 6.00 and 25 °C exhibited a positive shift of 20 mV relative to that of the wild-type HT, i.e., 245 mV, in an entropic manner. Because these two proteins have similar enthalpically stabilizing interactions, the difference in the entropic contribution to the Em value between them is likely to be due to the effect of the conformational alteration of the axial Met side chain associated with the inversion of the stereochemistry around the Sδ atom due to the effect of mutation on the internal mobility of the loop bearing the axial Met. Thus, the present study demonstrated that the internal mobility of the loop bearing the axial Met, relevant to entropic control of the redox function of the protein, is affected quite sensitively by the contextual stereochemical packing of amino acid side chains in the proximity of the axial Met. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
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