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Yoshinobu Ishikawa

Publications and source records attributed to Yoshinobu Ishikawa.

14 recordsLinked to original sources
PubMed2006

[Measurement of area of surplus X-ray radiation by dose-area product meter at image intensifier in angiography X-ray units].

The aim of this study was to assess the area of surplus X-ray radiation (surplus area) of three image intensifiers (I.I.) of two angiography X-ray units. Surplus area refers to an area surrounded with a circular collimator and effective field of view (FOV). Dose-area product (DAP) was used to measure surplus X-rays. A ratio of surplus area when based on each FOV showed an 8% to 39.3% increase with expansion of FOV, surplus area showed an 18 cm(2) to 95 cm(2) decrease with FOV. When the circular collimator was narrowed to a degree that could be confirmed partially in effective FOV, the rate of surplus area was decreased almost as much as the rate of scattered radiation. Surface dose was almost unchanged. The radiation exposure of the physician as well as that of the patient was reduced by the reduction of surplus area. The DAP meter, while a tool for patient radiation exposure management, is also highly useful for machinery management such as the measurement of surplus area at the I.I. system.

Angiography↗
PubMed2006

Molecular modeling of anti-parallel G-quadruplex DNA/TMPyP complexes.

We carried out the molecular modeling of anti-parallel G-quadruplex/TMPyP complex, molecular dynamics simulation and estimation of binding free energy using MM-PBSA method to validate groove binding model in addition to external stacking one. We found that not total electrostatic but van der Waals energy contributes to the negative binding free energies in both models.

DNA↗
PubMed2005

Stabilization of guanine quadruplex DNA by the binding of porphyrins with cationic side arms.

Many aromatic ligands, including tetra-(N-methyl-4-pyridyl)porphyrin (TMPyP4), have been reported to bind and stabilize quadruplex structure of telomeric DNA. We synthesized novel quadruplex-interacting porphyrins with cationic pyridinium and trimethylammonium arms at para- or meta-position of all phenyl groups of tetratolyl porphyrin. An antiparallel quadruplex structure was found to be stabilized more greatly by the meta-isomers than by the para-isomers and well-studied TMPyP4, as revealed by the increase in melting temperature of the quadruplex. One mole equivalent of the isomers was sufficient to stabilize the quadruplex. From the results of absorption, induced circular dichroism, and fluorescence resonance energy transfer spectroscopic methods, the unique site for the porphyrin binding is suggested to be the external guanine tetrad or groove of the quadruplex. The cationic side arms played a key role in the stabilization of the quadruplex structure.

Cations↗
PubMed2005

Mechanism of formation of iron(II) complexes with pentadentate ligands via C-C bond formation between trans-[Fe(2,4-bis(2-pyridylmethylimino)pentane)(MeCN)2]ClO4]2.MeCN and various nitriles.

The order of relative reactivity of nitriles for the formation of Fe(II) complexes (2s) with 3-(1-alkyl(or aryl)methyl)-1-imino-2,4-bis(2-pyridylmethylimine)(L(2)s) from that with 2,4-bis(2-pyridylmethylimono)pentane (L1), trans-[FeL(1)(MeCN)(2)][ClO(4)](2).MeCN (1), and various nitriles has been determined based on the following order: C(6)F(5)CN > 3,4-difluorobenzonitrile > 4-fluorobenzonitrile > C(6)H(5)CN > C(6)H(5)CH(2)CN > C(2)H(5)CN > MeCN > Me(2)CHCN >>Me(3)CN. An iron(II) complex with L1 in a cis-configuration was prepared as the ternary complex [FeL(1)(bpy)][ClO(4)](2).1.5MeNO(2).0.5H(2)O, 3a (bpy = bipyridine). Compounds 2s and 3a undergo enantiomeric interconversion with an activation energy of ca. 60 kJ mol(-1).

Ferrous Compounds↗
PubMed2004

The C-helix in CooA rolls upon CO binding to ferrous heme.

CooA is a homodimeric transcriptional activator from Rhodospirillum rubrum containing one heme in each subunit. CO binding to the heme in its sensor domain activates CooA, facilitating the binding to DNA by its DNA-binding domain. The C-helix links the two domains and shapes an interface between the subunits. To probe the nature of CO activation, residues at positions 112-121 on the C-helix were replaced by Asn or Gln and their effects were evaluated by resonance Raman spectroscopy and by the measurements of CO binding affinity. The nu(Fe-CO) stretching Raman line in CO-bound wild-type CooA was up-shifted by 6 cm(-1) in the L116Q, G117N, and L120Q mutants, indicating unequivocally that these residues are close to the bound CO. Residues Leu116 and Leu120 from each subunit form contacts with the corresponding residues in the opposite subunit, enabling hydrophobic interactions in the inactive ferrous form. Thus, in the CO-bound activated form, both C-helices appear to roll to direct these residues toward the heme, forming a hydrophobic pocket for the bound CO. The CO affinity is approximately one order of magnitude higher in the L112Q, I115Q, L116Q, G117N, L120Q, and T121N mutants but reduced in A114N mutant. The variation indicates that these residues are close to the heme in the ferrous and/or CO-bound forms and are responsible for CooA activation. A roll-and-slide mechanism is proposed for CO activation of CooA.

Bacterial Proteins↗
PubMed2004

Roles of heme axial ligands in the regulation of CO binding to CooA.

CooA is a CO-dependent transcription factor of the bacterium Rhodospirillum rubrum that contains a six-coordinate heme. It has as its heme axial ligands Pro(2) and Cys(75) in the ferric state and Pro(2) and His(77) in the ferrous state. To probe the regulation of CO binding and the ligand switching mechanism in CooA, we have prepared site-directed mutants in which the residues contributing the axial ligands are substituted. The properties of these mutants were investigated by resonance Raman and CO titration methods. Wild-type CooA binds CO with a modest dissociation constant (K(d)) of 11 microm, this value being typical for gas-sensing heme proteins. The K(d) value was greatly decreased in the P2H mutant, indicating that Pro(2) coordination fine tunes CO sensing in CooA. The bound CO in P2H gives rise to a nu(Fe-CO) stretching Raman line at 490 cm(-1), which is similar to that in wild-type CooA. Thus, Pro(2) is the ligand that is replaced by exogenous CO. In the H77A mutant, equilibrium CO binding is biphasic, and at high CO pressures two CO molecules occupy both axial sites. The nu(Fe-CO) stretching Raman line for the first CO molecule was observed at 497 cm(-1). Some of the His(77) mutants showed an additional nu(Fe-CO) line at 525 cm(-1). The binding affinity of the second CO molecule correlates with the five-coordinate component in the ferrous His(77) mutants and also with the acidity of the side chain at position 77. Thus, we propose the Cys(75)-His(77) ligand switch is controlled by His(77) acting as a proton reservoir.

Amino Acid Sequence↗
PubMed2003

Residues in the distal heme pocket of neuroglobin. Implications for the multiple ligand binding steps.

Amino acid residues in the ligand binding pocket of human neuroglobin have been identified by site-directed mutagenesis and their properties investigated by resonance Raman and flash photolysis methods. Wild-type neuroglobin has been shown to have six-coordinate heme in both ferric and ferrous states. Substitution of His96 by alanine leads to complete loss of heme, indicating that His96 is the proximal ligand. The resonance Raman spectra of M69L and K67T mutants were similar to those of wild-type (WT) neuroglobin in both ferric and ferrous states. By contrast, H64V was six-coordinate high-spin and five-coordinate high-spin in the ferric and ferrous states, respectively, at acidic pH. The spectra were pH-dependent and six-coordinate with the low-spin component dominating at alkaline pH. In a double mutant H64V/K67T, the high-spin component alone was detected in the both ferric and the ferrous states. This implies that His64 is the endogenous ligand and that Lys67 is situated nearby in the distal pocket. In the ferrous H64V and H64V/K67T mutants, the nu(Fe-His) stretching frequency appears at 221 cm(-1), which is similar to that of deoxymyoglobin. In the ferrous CO-bound state, the nu(Fe-CO) stretching frequency was detected at 521 and 494 cm(-1) in WT, M69L, and K67T, while only the 494 cm(-1) component was detected in the H64V and H64V/K67T mutants. Thus, the 521 cm(-1) component is attributed to the presence of polar His64. The CO binding kinetics were biphasic for WT, H64V, and K67T and monophasic for H64V/K67T. Thus, His64 and Lys67 comprise a unique distal heme pocket in neuroglobin.

Amino Acid Sequence↗
PubMed2003

Inversion of axial coordination in myoglobin to create a "proximal" ligand binding pocket.

A ligand binding pocket has been created on the proximal side of the heme in porcine myoglobin by site-directed mutagenesis. Our starting point was the H64V/V68H double mutant which has been shown to have bis-histidine (His68 and His93) heme coordination [Dou, Y., Admiraal, S. J., Ikeda-Saito, M., Krzywda, S., Wilkinson, A. J., Li, T., Olson, J. S., Prince, R. C., Pickering, I. J., George, G. N. (1995) J. Biol. Chem. 270, 15993-16001]. The replacement of the proximal His93 ligand by noncoordinating Ala (H64V/V68H/H93A) or Gly (H64V/V68H/H93G) residues resulted unexpectedly in a six-coordinate low-spin species in both ferric and ferrous states. To test the hypothesis that the sixth coordinating ligand in the triple mutants was the imidazole of His97, this residue was mutated to Phe, in the quadruple mutants, H64V/V68H/H93A/H97F and H64V/V68H/H93G/H97F. The ferric quadruple mutants show a clear water/hydroxide alkaline transition and high cyanide and CO affinities, characteristics similar to those of wild-type myoglobin. The nu(Fe-CO) and nu(C-O) stretching frequencies in the ferrous-CO state of the quadruple mutants indicate that the "proximal" ligand binding heme pocket is less polar than the distal pocket in the wild-type protein. Thus, we conclude that the proximal heme pocket in the quadruple mutants has a similar affinity for exogenous ligands to the distal pocket of wild-type myoglobin but that the two pockets have different polarities. The quadruple mutants open up new approaches for developing heme chemistry on the myoglobin scaffold.

Amino Acid Substitution↗
PubMed2003

Self-aggregation inhibits the photonuclease activity of porphyrins.

A series of tentacle porphyrins having four aminoalkyl groups at the periphery was synthesized, and the DNA binding properties were investigated by absorption and circular dichroism (CD) spectroscopic methods. The aminopropyl chain was found to facilitate binding, and bisignate induced CD spectra revealed that the porphyrins are self-stacked on the DNA surface. The photonuclease activity of the tentacle porphyrins was also studied, and the aminopropylporphyrin showed the highest activity. The activity increased in proportion to the porphyrin load, but higher loads resulted in the decrease of activity. This inhibitory step corresponded to aggregation of the porphyrin. Thus, the aggregation was suggested to shield the inner porphyrin from the solvent, the production of active oxygen species being suppressed.

DNA↗
PubMed2003

[Dose evaluation of a flat-panel detector system].

We compared the INNOVA2000 (INNOVA), which has a flat panel detector system, and the Advantx LCLP (LCLP), which has a conventional I. I. system, in terms of the dependence of phantom thickness on patient surface dose (surface dose) and receptor entrance dose (entrance dose). We examined the reduction in surface dose and entrance dose by using an additional filter and shortening the patient detector distance (PDD). The surface dose rate for fluoroscopy with INNOVA was 73.8-63.5%, and the reduction rate was high at a phantom thickness of less than 20 cm compared with LCLP, but such a reduction could not be expected at a phantom thickness of more than 30 cm, depending on maximum dose rate. The rate of reduction in surface dose in the case of exposure was considerably low at a phantom thickness of about 20 cm, while the other's (5, 10, 15, 25, 30 cm) reduction rates were about 40%. The length of PDD with INNOVA was shortened by 5 cm compared with LCLP. As a result, we obtained a reduction rate of surface dose of 11-15%, while the entrance dose was 10% lower. The reduction rate achieved with an additional filter was 43-60% in surface dose rate in fluoroscopy, whereas that of surface dose for exposure was about 50% at phantom thicknesses up to 20 cm, but remained just 25% thereafter. The results indicated that the reduction of surface dose with INNOVA could be changed by means of the phantom thickness, and we consider the effect achieved by the addition of a filter to be the main factor.

Cardiovascular System↗
PubMed2002

Copper insertion facilitates water-soluble porphyrin binding to rA.rU and rA.dT base pairs in duplex RNA and RNA.DNA hybrids.

The binding of the copper(II) complex of water-soluble meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to double-helical polynucleotides has been studied by optical absorption, circular dichroism (CD), and resonance Raman spectroscopic methods. The target polymers were RNA and RNA.DNA hybrids consisting of rA.rU, rI.rC, rA.dT, and rI.dC base pairs. Relative to the metal-free H(2)TMPyP [Uno, T., Hamasaki, K., Tanigawa, M., and Shimabayashi, S. (1997) Inorg. Chem. 36, 1676-1683], CuTMPyP binds to poly(rA).poly(dT) and poly(rA).poly(rU) with a greatly increased binding constant. The external self-stacking of the porphyrin on the surface of the polymers was evident from the strong conservative-type induced CD signals. The signal intensity correlated almost linearly with the number of stacking sites on the polymer except for poly(rA).poly(dT), which showed extraordinarily strong CD signals. Thus, the bound porphyrin may impose an ordered architecture on the polymer surface, the stacking being facilitated by the more planar nature of the CuTMPyP than the nonmetal counterpart. Resonance Raman spectra of the stacked CuTMPyP were indistinguishable from those of the intercalated one with positive delta(Cbeta-H) and negative delta(Cm-Py) bending shifts, and hence the stacked porphyrins are suggested to adopt a similar structure to that of intercalated ones. Porphyrin flattening by copper insertion opens a new avenue for medical applications of porphyrins, blocking biological events related to RNA and hybrids in malignant cells.

Base Pairing↗
PubMed2002

Potent DNA photocleavage by zinc(II) complexes of cationic bis-porphyrins linked with aliphatic diamine.

We have prepared zinc(II) complexes of cationic bis-porphyrins, as one of the attempts to improve less DNA photocleavage activities of the metal-free bis-porphyrins composed of two H(2)TMPyP-like chromophores, linked with a series of aliphatic diamines. The less activities seemed to be derived from their intermolecular self-aggregation properties in aqueous solution. The zinc(II) insertion into the metal-free cationic bis-porphyrins completely removed their self-aggregation properties, most probably due to steric hindrance between axial ligands of zinc(II) chromophores of the cationic bis-porphyrins. The DNA photocleavage activities of the zinc(II) complexes were fully enhanced, which were three times larger than that of the lead compound H(2)TMPyP. Quantitative analysis of singlet oxygen production by photosensitization of cationic bis-porphyrins was performed using 1,3-diphenylisobenzofuran, and the singlet oxygen productivities of them were found to be related to their solution properties. There is a good relationship between the activities and the productivities, which will provide insights into the further development of more effective DNA photocleavage agents.

Cations↗
PubMed1999

New Robust Bleomycin Analogues: Synthesis, Spectroscopy, and Crystal Structures of the Copper(II) Complexes.

Two new bleomycin analogues, 2-[((2-(4-imidazolyl)ethyl)amino)carbonyl]-6-[((2-amino-2-methylpropyl)amino)methyl]pyridine = L(3)() and 2-[((2-(4-imidazolyl)ethyl)amino)carbonyl]-6-[((2-amino-1,1,2-trimethylpropyl)amino)methyl]pyridine = L(4)(), were synthesized in order to create air-stable ligands of their Cu(I) (and Fe(II)) complexes. The protonation constants (log K(n)()) of the ligands at 25 degrees C and I = 0.1 M NaNO(3) were 9.9, 6.9, and 5.2 for L(3)() and 10.0, 6.7, and 3.9 for L(4)(). The complexation of the triprotonated L(3)() and L(4)() with Cu(II) started at pH < 5 to yield 4-coordinate [Cu(II)(H(-)(1)L).H(+)](2+) complexes, 4 and 6, respectively, followed by formation of square-pyramidal [Cu(II)(H(-)(1)L)](+) complexes, 5 and 7, with pK(a) values of 5.6 for 5 and 5.9 for 7. The complexation constants, log K(Cu)()II(H)()-1(L), were 8.9 for [Cu(II)(H(-)(1)L(3))](+), 5, and 8.6 for [Cu(II)(H(-)(1)L(4))](+), 7, respectively. The structures of [Cu(II)(H(-)(1)L(3))]ClO(4) (5.ClO(4)) and [Cu(II)(H(-)(1)L(4))]BF(4) (7.BF(4)) were determined by X-ray crystallography. Crystal data for 5.ClO(4): monoclinic, space group P2(1)/n (No. 14), a = 13.978(6) Å, b = 8.103(3) Å, c = 18.037(5) Å, beta = 98.61(3) degrees, V = 2019(1) Å(3), Z = 4, R = 0.053, and R(w) = 0.044 for 2996 [I > 3sigma(I)] reflections. Crystal data for 7.BF(4): monoclinic, space group P2(1)/n (No. 14), a = 16.092 (4) Å, b = 7.974(4) Å, c = 16.819(2) Å, beta = 99.64(1) degrees, V = 2127(1) Å(3), Z = 4, R = 0.040, and R(w) = 0.025 for 1633 [I > 4sigma(I)] reflections. The coordination geometry around the copper was a distorted square-pyramid in 5, while that of 7 was the intermediate between a trigonal-bipyramid and a square-pyramid. The distortion is influenced strongly by the number of the methyl group. The EPR spectral data for both copper(II) complexes were consistent with the retention of the solid-state structure in frozen DMF/MeOH (1:1) solution at 77 K. The visible absorption spectra of 10% DMF/aqueous solutions (pH 9.5) of 5 and 7 at I = 0.1 M NaNO(3) showed absorption maxima at 646 nm with a shoulder at ca. 900 nm for 5 and at 658 and 888 nm for 7. The red-shift of 7 by ca. 12 nm relative to 5 reflects the distortion toward the trigonal-bipyramidal geometry of 7 in solution. Both complexes displayed irreversible redox behavior in DMF at I = 0.1 M tetra(n-butyl)ammonium tetrafluoroborate. The anodic and cathodic peak potentials obtained by cyclic voltammetry for 5 and 7 were -0.14 and -0.76 V for 5 and -0.17 and -0.80 for 7 vs Ag/AgCl. The cathodic potentials of copper(II) complexes were shifted toward the anodic direction by ca. 20-60 mV compared to the nonsubstituted 5-coordinate, [Cu(II)(H(-)(1)L(1))](+) complex, 16 (-0.82 V vs Ag/AgCl). The Cu(I) complexes (9and 10) are air-oxidized to the corresponding Cu(II) complexes, 5 and 7, respectively.

Journal Article↗