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Yoshihito Watanabe

Publications and source records attributed to Yoshihito Watanabe.

At least 37 records · Page 2Linked to original sources
PubMed2004

Interaction of plastocyanin with oligopeptides: effect of lysine distribution within the peptide.

We synthesized and purified four oligopeptides containing four lysines (KKKK, GKKGGKK, KKGGGKK, and KGKGKGK) as models for the plastocyanin (PC) interacting site of cytochrome f. These peptides competitively inhibited electron transfer between cytochrome c and PC. The inhibitory effect increased as the peptide concentrations were increased. The association constants between PC and the peptides did not differ significantly (3500-5100 M(-1)), although the association constant of PC-KGKGKGK was a little larger than the constants between PC and other peptides. Changes in the absorption spectrum of PC were observed when the peptides were added to the PC solution: peaks and troughs were detected at about 460 and 630 nm and at about 560 and 700 nm, respectively, in the difference absorption spectra between the spectra with and without peptides. These changes were attributed to the structural change at the copper site of PC by interaction with the peptides. The structural change was most significant when tetralysine was used. These results show that binding of the oligopeptide to PC is slightly more efficient when lysines are distributed uniformly within the peptide, whereas the structural change of PC becomes larger when the lysines are close to each other within the peptide.

Amino Acid Sequence↗
PubMed2003

Molecular engineering of myoglobin: influence of residue 68 on the rate and the enantioselectivity of oxidation reactions catalyzed by H64D/V68X myoglobin.

In the elucidation of structural requirements of heme vicinity for hydrogen peroxide activation, we found that the replacement of His-64 of myoglobin (Mb) with a negatively charged aspartate residue enhanced peroxidase and peroxygenase activities by 78- and 580-fold, respectively. Since residue 68 is known to influence the ligation of small molecules to the heme iron, we constructed H64D/V68X Mb bearing Ala, Ser, Leu, Ile, and Phe at position 68 to improve the oxidation activity. The Val-68 to Leu mutation of H64D Mb accelerates the reaction with H(2)O(2) to form a catalytic species, called compound I, and improves the one-electron oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) (i.e., peroxidase activity) approximately 2-fold. On the other hand, H64D/V68I Mb oxygenates thioanisole 2.7- and 1600-fold faster than H64D and wild-type Mb, respectively. In terms of the enantioselectivity, H64D/V68A and H64D/V68S Mb were good chiral catalysts for thioanisole oxidation and produced the (R)-sulfoxide dominantly with 84% and 88% ee, respectively [Kato, S., et al. (2002) J. Am. Chem. Soc. 124, 8506-8507]. On the contrary, the substitution of Val-68 in H64D Mb with an isoleucine residue alters the dominant sulfoxide product from the (R)- to the (S)-isomer. The crystal structures of H64D/V68A and H64D/V68S Mb elucidated in this study do not clearly indicate residues interacting with thioanisole. However, comparison of the active site structures provides the basis to interpret the changes in oxidation activity: (1) direct steric interactions between residue 68 and substrates (i.e., H(2)O(2), ABTS, thioanisole) and (2) the polar interactions between tightly hydrogen-bonded water molecules and substrates.

Amino Acid Substitution↗
PubMed2003

Mechanisms of hydrogen-, oxygen-, and electron-transfer reactions of cumylperoxyl radical.

Rates of hydrogen-transfer reactions from a series of para-substituted N,N-dimethylanilines to cumylperoxyl radical and oxygen-transfer reactions from cumylperoxyl radical to a series of sulfides and phosphines have been determined in propionitrile (EtCN) and pentane at low temperatures by use of ESR. The observed rate constants exhibit first-order and second-order dependence with respect to concentrations of N,N-dimethylanilines. This indicates that the hydrogen- and oxygen-transfer reactions proceed via 1:1 charge-transfer (CT) complexes formed between the substrates and cumylperoxyl radical. The primary kinetic isotope effects are determined by comparing the rates of N,N-dimethylanilines and the corresponding N,N-bis(trideuteriomethyl)anilines. The isotope effect profiles are quite different from those reported for the P-450 model oxidation of the same series of substrates. Rates of electron-transfer reactions from ferrocene derivatives to cumylperoxyl radical have also been determined by use of ESR. The catalytic effects of Sc(OTf)(3) (OTf = triflate) on the electron-transfer reactions are compared with those of Sc(OTf)(3) on the hydrogen- and oxygen-transfer reactions. Such comparison provides strong evidence that the hydrogen- and oxygen- transfer reactions of cumylperoxyl radical proceed via a one-step hydrogen atom and oxygen atom transfer rather than via an electron transfer from substrates to cumylperoxyl radical.

Journal Article↗
PubMed2003

Isolation and crystal structure of a water-soluble iridium hydride: a robust and highly active catalyst for acid-catalyzed transfer hydrogenations of carbonyl compounds in acidic media.

This paper reports the isolation and structural determination of a water-soluble hydride complex [Cp*Ir(III)(bpy)H](+) (1, Cp* = eta(5)-C(5)Me(5), bpy = 2,2'-bipyridine) that serves as a robust and highly active catalyst for acid-catalyzed transfer hydrogenations of carbonyl compounds at pH 2.0-3.0 at 70 degrees C. The catalyst 1 was synthesized from the reaction of a precatalyst [Cp*Ir(III)(bpy)(OH(2))](2+) (2) with hydrogen donors HCOOX (X = H or Na) in H(2)O under controlled conditions (2.0 < pH < 6.0, 25 degrees C) which avoid protonation of the hydrido ligand of 1 below pH ca. 1.0 and deprotonation of the aqua ligand of 2 above pH ca. 6.0 (pK(a) value of 2 = 6.6). X-ray analysis shows that complex 1 adopts a distorted octahedral geometry with the Ir atom coordinated by one eta(5)-Cp*, one bidentate bpy, and one terminal hydrido ligand that occupies a bond position. The isolation of 1 allowed us to investigate the robust ability of 1 in acidic media and reducing ability of 1 in the reaction with carbonyl compounds under both stoichiometric and catalytic conditions. The rate of the acid-catalyzed transfer hydrogenation is drastically dependent on pH of the solution, reaction temperature, and concentration of HCOOH. The effect of pH on the rate of the transfer hydrogenation is rationalized by the pH-dependent formation of 1 and activation process of the carbonyl compounds by protons. High turnover frequencies of the acid-catalyzed transfer hydrogenations at pH 2.0-3.0 are ascribed not only to nucleophilicity of 1 toward the carbonyl groups activated by protons but also to a protonic character of the hydrido ligand of 1 that inhibits the protonation of the hydrido ligand.

Journal Article↗
PubMed2002

Structural and spectroscopic features of a cis (hydroxo)-Fe(III)-(carboxylato) configuration as an active site model for lipoxygenases.

In our preliminary communication (Ogo, S.; Wada, S.; Watanabe, Y.; Iwase, M.; Wada, A.; Harata, M.; Jitsukawa, K.; Masuda, H.; Einaga, H. Angew. Chem., Int. Ed. 1998, 37, 2102-2104), we reported the first example of X-ray analysis of a mononuclear six-coordinate (hydroxo)iron(III) non-heme complex, [Fe(III)(tnpa)(OH)(RCO(2))]ClO(4) [tnpa = tris(6-neopentylamino-2-pyridylmethyl)amine; for 1, R = C(6)H(5)], which has a characteristic cis (hydroxo)-Fe(III)-(carboxylato) configuration that models the cis (hydroxo)-Fe(III)-(carboxylato) moiety of the proposed (hydroxo)iron(III) species of lipoxygenases. In this full account, we report structural and spectroscopic characterization of the cis (hydroxo)-Fe(III)-(carboxylato) configuration by extending the model complexes from 1 to [Fe(III)(tnpa)(OH)(RCO(2))]ClO(4) (2, R = CH(3); 3, R = H) whose cis (hydroxo)-Fe(III)-(carboxylato) moieties are isotopically labeled by (18)OH(-), (16)OD(-), (18)OD(-), (12)CH(3)(12)C(18)O(2)(-), (12)CH(3)(13)C(16)O(2)(-), (13)CH(3)(12)C(16)O(2)(-), (13)CH(3)(13)C(16)O(2)(-), and H(13)C(16)O(2)(-). Complexes 1-3 are characterized by X-ray analysis, IR, EPR, and UV-vis spectroscopy, and electrospray ionization mass spectrometry (ESI-MS).

Acetates↗
PubMed2002

Asymmetric sulfoxidation and amine binding by H64D/V68A and H64D/V68S Mb: mechanistic insight into the chiral discrimination step.

The H64D/V68A and H64D/V68S mutants of Myoglobin are found to oxidize thioanisole with high enantioselectivity and reactivity. These mutants are also capable of enantioselective binding of alpha-methylbenzylamine, which mimics an expected sulfoxidation intermediate. The kinetic study of the amine binding shows that the Fe-O bond cleavage in the intermediate may be the chiral discrimination step of the sulfoxidation.

Kinetics↗
PubMed2002

Reactivity of hydroperoxide bound to a mononuclear non-heme iron site.

The first isolation and spectroscopic characterization of the mononuclear hydroperoxo-iron(III) complex [Fe(H(2)bppa)(OOH)](2+) (2) and the stoichiometric oxidation of substrates by the mononuclear iron-oxo intermediate generated by its decomposition have been described. The purple species 2 obtained from reaction of [Fe(H(2)bppa)(HCOO)](ClO(4))(2) with H(2)O(2) in acetone at -50 degrees C gave characteristic UV-vis (lambda(max) = 568 nm, epsilon = 1200 M(-1) cm(-1)), ESR (g = 7.54, 5.78, and 4.25, S = (5)/(2)), and ESI mass spectra (m/z 288.5 corresponding to the ion, [Fe(bppa)(OOH)](2+)), which revealed that 2 is a high-spin mononuclear iron(III) complex with a hydroperoxide in an end-on fashion. The resonance Raman spectrum of 2 in d(6)-acetone revealed two intense bands at 621 and 830 cm(-1), which shifted to 599 and 813 cm(-1), respectively, when reacted with (18)O-labeled H(2)O(2). Reactions of the isolated (bppa)Fe(III)-OOH (2) with various substrates (single turnover oxidations) exhibited that the iron-oxo intermediate generated by decomposition of 2 is a nucleophilic species formulated as [(H(2)bppa)Fe(III)-O*].

Alkanes↗
PubMed2002

pH-dependent H2-activation cycle coupled to reduction of nitrate ion by CpIr complexes.

This paper reports a pH-dependent H2-activation [H2 (pH 1-4) --> H+ + H- (pH -1) --> 2H+ + 2e-] promoted by CpIr complexes [Cp = eta5-C5(CH3)5]. In a pH range of about 1-4, an aqueous HNO3 solution of [CpIr(III)(H2O)3]2+ (1) reacts with 3 equiv of H2 to yield a solution of [(CpIr(III))2(mu-H)3]+ (2) as a result of heterolytic H2-activation [2[1] + 3H2 (pH 1-4) --> [2] + 3H+ + 6H2O]. The hydrido ligands of 2 display protonic behavior and undergo H/D exchange with D+: [M-(H)3-M]+ + 3D+ <==>[M-(D)3-M]+ + 3H+ (where M = CpIr). Complex 2 is insoluble in a pH range of about -0.2 (1.6 M HNO3/H2O) to -0.8 (6.3 M HNO3/H2O). At pH -1 (10 M HNO3/H2O), a powder of 2 drastically reacts with HNO3 to give a solution of [CpIr(III)(NO3)2] (3) with evolution of H2, NO, and NO2 gases. D-labeling experiments show that the evolved H2 is derived from the hydrido ligands of 2. These results suggest that oxidation of the hydrido ligands of 2 [[2] + 4NO3- (pH -1) --> 2[3] + H2 + H+ + 4e-] couples to reduction of NO3- (NO3- --> NO2- --> NO). To complete the reaction cycle, complex 3 is transformed into 1 by increasing the pH of the solution from -1 to 1. Therefore, we are able to repeat the reaction cycle using 1, H2, and a pH gradient between 1 and -1. A conceivable mechanism for the H2-activation cycle with reduction of NO3- is proposed.

Journal Article↗
PubMed2002

(Catecholato)iron(III) complexes: structural and functional models for the catechol-bound iron(III) form of catechol dioxygenases.

Catechol dioxygenases are mononuclear non-heme iron enzymes that catalyze the oxygenation of catechols to aliphatic acids via the cleavage of aromatic rings. In the last 20 years, a number of (catecholato)iron(III) complexes have been synthesized and characterized as structural and functional models for the catechol-bound iron(III) form of catechol dioxygenases. This review focuses on the structural and spectroscopic characteristics and oxygenation activity of the title complexes.

Catechol 1,2-Dioxygenase↗
PubMed2002

Construction of heme enzymes: four approaches.

Construction of enzymes that catalyze either desired reactions or exhibit desired substrate specificity is one of the goals of enzymatic study. Rational design of enzymes is an important approach in this field. Another, extremely different, methodology from rational design, directed evolution, has been rapidly developed over the past two years.

Binding Sites↗
PubMed2002

Reconstruction of two victims' posturing based on the induced radioactivities in their bones in the criticality accident in Tokai-Mura, Japan.

On 30 September 1999, three workers were severely exposed to neutrons and gamma rays in a criticality accident that occurred at a uranium conversion facility in Tokai-mura, Ibaraki Prefecture, Japan. Radiochemical analyses of 32P and 45Ca induced by neutrons in bone matrix were carried out after the deaths of two of the victims. It was found that more than several million becquerels of both nuclides had been produced in their body skeletons. Results showed non-homogeneous distributions of neutron fluence in the bodies, from which it could be deduced how both workers were positioned relative to the fission source during exposure, i.e., at the moment of the first nuclear excursion. For the victim who died first, the activities in the central part of his body were more than those of his extremities. Also, in the central part of his body, the right side showed more activities than the left side. As for the second man, the activities indicated rather uniform exposure to neutrons to the whole body although the geometrical distribution of the activity varied enough to assume his orientation. Such information on the geometrical distribution of neutron-induced radioactivities in the skeleton can be used to reconstruct the posturing of the victims, which is necessary to estimate their apparent absorbed doses.

Bone and Bones↗
PubMed1998

A New, Aqueous (1)H NMR Shift Reagent Based on Host-Guest Molecular Recognition Principles for Organic Compound Structural Analysis: Non-covalent pi-pi and Hydrophobic Interactions Using a Supramolecular Host, [CpRh(2'-deoxyadenosine)](3)(OTf)(3).

We have discovered that the supramolecular host [CpRh(2'-deoxyadenosine)](3)(OTf)(3) (1, Cp = eta(5)-C(5)Me(5), OTf = CF(3)SO(3)(-)) has utility as a new, aqueous (1)H NMR shift reagent, via a host-guest molecular recognition process that occurs by non-covalent pi-pi and hydrophobic interactions, with a wide variety of H(2)O-soluble organic substrates. These organic compound guests that we present, to illustrate the utility of host 1 as a novel, aqueous (1)H NMR shift reagent, encompass examples such as aromatic carboxylic acids, phenylacetic acid (G1), 1-naphthoic acid (G2), and 2-naphthoic acid (G3), an aliphatic carboxylic acid, cyclohexylacetic acid (G4), as well as biological compounds, a di- and a tetrapeptide containing terminal L-tryptophan (Trp) or L-phenylalanine (Phe) groups, L-Trp-L-Phe (G5) and L-Trp-L-Met-L-Asp-L-Phe amide (G6) in the pH range 5-10. A discussion of the molecular recognition parameters that effect the (1)H NMR shifts of the organic guests and a comparison with the water-soluble lanthanide shift reagents (LSRs) will be presented to demonstrate the usefulness of this aqueous molecular receptor as an aid for organic compound structural analysis.

Journal Article↗