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Toshimasa Ishida

Publications and source records attributed to Toshimasa Ishida.

At least 19 recordsLinked to original sources
PubMed2006

Quantitative evaluation of each catalytic subsite of cathepsin B for inhibitory activity based on inhibitory activity-binding mode relationship of epoxysuccinyl inhibitors by X-ray crystal structure analyses of complexes.

To quantitatively estimate the inhibitory effect of each substrate-binding subsite of cathepsin B (CB), a series of epoxysuccinyl derivatives with different functional groups bound to both carbon atoms of the epoxy ring were synthesized, and the relationship between their inhibitory activities and binding modes at CB subsites was evaluated by the X-ray crystal structure analyses of eight complexes. With the common reaction in which the epoxy ring of inhibitor was opened to form a covalent bond with the SgammaH group of the active center Cys29, the observed binding modes of the substituents of inhibitors at the binding subsites of CB enabled the quantitative assessment of the inhibitory effect of each subsite. Although the single blockage of S1' or S2' subsite exerts only the inhibitory effect of IC50 = approximately 24 microM (k2 = approximately 1250 M(-1) s(-1)) or approximately 15 microM (k2 = approximately 1800 M(-1) s(-1)), respectively, the synchronous block of both subsites leads to IC50 = approximately 23 nM (k2 = 153,000 - 185,000 M(-1) s(-1)), under the condition that (i) the inhibitor possesses a P1' hydrophobic residue such as Ile and a P2' hydrophobic residue such as Ala, Ile or Pro, and (ii) the C-terminal carboxyl group of a P2' residue is able to form paired hydrogen bonds with the imidazole NH of His110 and the imidazole N of His111 of CB. The inhibitor of a Pn' > or = 3' substituent was not potentiated by collision with the occluding loop. On the other hand, it was suggested that the inhibitory effects of Sn subsites are independent of those of Sn' subsites, and the simultaneous blockage of the funnel-like arrangement of S2 and S3 subsites leads to the inhibition of IC50 = approximately 40 nM (k2 = approximately 66,600 M(-1) s(-1)) regardless of the lack of Pn' substituents. Here we present a systematic X-ray structure-based evaluation of structure-inhibitory activity relationship of each binding subsite of CB, and the results provide the structural basis for designing a more potent CB-specific inhibitor.

Animals↗
PubMed2006

Laser control of reactions of photoswitching functional molecules.

Laser control schemes of reactions of photoswitching functional molecules are proposed based on the quantum mechanical wave-packet dynamics and the design of laser parameters. The appropriately designed quadratically chirped laser pulses can achieve nearly complete transitions of wave packet among electronic states. The laser parameters can be optimized by using the Zhu-Nakamura theory of nonadiabatic transition. This method is effective not only for the initial photoexcitation process but also for the pump and dump scheme in the middle of the overall photoswitching process. The effects of momentum of the wave packet crossing a conical intersection on the branching ratio of products have also been clarified. These control schemes mentioned above are successfully applied to the cyclohexadiene/hexatriene photoisomerization (ring-opening) process which is the reaction center of practical photoswitching molecules such as diarylethenes. The overall efficiency of the ring opening can be appreciably increased by using the appropriately designed laser pulses compared to that of the natural photoisomerization without any control schemes.

Journal Article↗
PubMed2006

Amine free crystal structure: the crystal structure of d(CGCGCG)2 and methylamine complex crystal.

We succeeded in the crystallization of d(CGCGCG)2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2Fo-Fc map was much clear and easily traced. It is the first time monoamine co-crystallizes with d(CGCGCG)2. However, methylamine was not found from the complex crystal of d(CGCGCG)2 and methylamine. Five Mg ions were found around d(CGCGCG)2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg2+. DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG)2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this.

Crystallography, X-Ray↗
PubMed2006

Effect of N-terminal region of eIF4E and Ser65-phosphorylation of 4E-BP1 on interaction between eIF4E and 4E-BP1 fragment peptide.

To clarify the contribution of N-terminal region of eukaryotic initiation factor 4E (eIF4E) to the interaction with 4E-BP and to investigate the effect of 4E-BP phosphorylation on the interaction with eIF4E, the interaction profiles of the Ser65-unphosphorylated and phosphorylated peptides (Thr37-Thr70 fragment of 4E-BP1) with full-length and N-terminal 33 residues-deleted eIF4Es were investigated by fluorescence and SPR methods. The effect of N-terminal region of eIF4E on the interaction with 4E-BP1 peptides was shown to be dependent on the interaction state, that is, the steady-state fluorescence and kinetic-state SRP analyses showed the positive and negative contributions of the N-terminal region to the interaction with the peptide, respectively, despite its unphosphorylated or phosphorylated state. The comparison of the association constants of the peptide with those of full-length 4E-BP1 indicated the importance of N-terminal (1-36) and/or C-terminal (71-118) sequence of 4E-BP1 for the interaction, although the MD simulations suggested that the alpha-helical region (Arg56-Cys62) of 4E-BP1 peptide is sufficient for keeping the interaction. The MD simulations also indicated that a charge-dependent rigid hydration shell formed around the phosphate group makes the molecular conformation rigid, and single Ser65 phosphorylation is insufficient for releasing 4E-PB1 peptide from eIF4E.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Tunneling splitting of energy levels and rotational constants in the vinyl radical C2H3.

The instanton theory newly implemented by two of the authors (G.V.M. and H.N.) is applied to hydrogen tunneling transfer in a vinyl radical. The converged instanton trajectory is found on the CCSD(T)/aug-cc-pVTZ level of an ab initio potential energy surface. The calculated ground-state energy splitting agrees with the recent high-resolution experimental data within 3% of discrepancy. The semiclassical wave function is used to estimate the splitting of the principal rotational constants of the radical.

Journal Article↗
PubMed2006

Binding mode of novel 1-substituted quinazoline derivatives to poly(ADP-ribose) polymerase-catalytic domain, revealed by X-ray crystal structure analysis of complexes.

In order to clarify the role of the 1-substituent of quinazoline derivatives in their inhibitory activity against poly(ADP-ribose) polymerase (PARP), two novel inhibitors, 1 [8-hydroxy-1-(3-morpholinopropyl)-quinazoline-2,4(1H,3H)-dione] and 2 [8-hydroxy-1-(3-phenoxypropyl)-quinazoline-2,4(1H,3H)-dione], were synthesized and subjected to X-ray crystal analysis in complex with the PARP C-terminal catalytic domain (PARP-CD), which requires NAD+ coenzyme for biological function. The nicotinamide-mimicking part of the quinazoline skeleton of 1 and 2 were both located at the nicotinamide subsite of the NAD+-binding pocket in the same manner as previously reported inhibitors: three hydrogen bonds [(Gly-863)NH-O12, (Gly-863)O-HN3 and (Ser-904)O(gamma)-O12] and stacking interaction between the Tyr-907 phenol and the quinazoline ring. On the other hand, the N-morpholinoprop-3-yl moiety introduced at the 1-position of the quinazoline ring in 1 bridged the large gap between the donor site and the acceptor site through a (Met-890)NH-O20(morpholine) hydrogen bond, where the donor and the acceptor sites are classified as the binding sites of NAD+ and the ADP moiety of the poly(ADP-ribose) chain, respectively. In contrast, the N-phenoxyprop-3-yl moiety in 2 formed hydrophobic interactions close to the adenosine-binding site of NAD+, unlike the hydrogen bond such as in 1. As the inhibitory activities of 1 and 2 for PARP were much more potent than those of the unsubstituted nicotinamide analogues, these results suggest that the occupation of the proximal region of the ADP phosphate-and adenosine-binding subsite of the donor site or that of the gap between the donor and the acceptor site by the 1-substituent of quinazoline may increase the inhibitory activity considerably. The nearly equal inhibitory activities of 1 and 2, despite of their different binding modes at the active site, indicate that this 1-substituent is promising in improving the bioavailability of the inhibitor without compromising its inhibitory activity.

Animals↗
PubMed2006

Fluorescence-coupled CD conformational monitoring of filament formation of tau microtubule-binding repeat domain.

To clarify the contribution of the three- or four-repeated peptide moiety in tau microtubule-binding domain (MBD) to paired helical filament (PHF) formation, conformational transition accompanied by heparin-induced filament formation was investigated stepwise for four repeat peptides (R1-R4), one three-repeated R1-R3-R4 peptide (3RMBD), and one four-repeated R1-R2-R3-R4 peptide (4RMBD) using a combination of thioflavin S fluorescence and circular dichroism (CD) measurements in a neutral buffer (pH 7.6). The comparison of the fluorescence profile of each repeat peptide with those of 3RMBD and 4RMBD showed the synergistic contribution of R1-R4 to PHF formation of MBD. The CD spectrum measured as a function of filament formation time indicates that: (i) two conformational transitions occur for the filament formations of R3 (from the random structure to the beta-sheet structure) and 3RMBD (from the random structure to the alpha-helix structure), (ii) the filament formations of R2 and 4RMBD proceed via the synchronized conformational transitions of the alpha-helix and random structures, and (iii) the filament formation of 4RMBD is dependent on the aggregation behavior of R2. These data are useful for elucidating the MBD conformational transition in tau PHF formation.

Amino Acid Sequence↗
PubMed2006

Ab initio nonadiabatic quantum dynamics of cyclohexadiene/hexatriene ultrafast photoisomerization.

Reaction mechanisms of the ultrafast photoisomerization between cyclohexadiene and hexatriene have been elucidated by the quantum dynamics on the ab initio potential energy surfaces calculated by multireference configuration interaction method. In addition to the quantum wave-packet dynamics along the two-dimensional reaction coordinates, the semiclassical analyses have also been carried out to correctly estimate the nonadiabatic transition probabilities around conical intersections in the full-dimensional space. The reaction time durations of radiationless decays in the wave-packet dynamics are found to be generally consistent with the femtosecond time-resolution experimental observations. The nonadiabatic transition probabilities among the ground (S0), first (S1), and second (S2) excited states have been estimated by using the semiclassical Zhu-Nakamura formula considering the full-dimensional wave-packet density distributions in the vicinity of conical intersections under the harmonic normal mode approximation. The cyclohexadiene (CHD) ring-opening process proceeds descending on the S1(1 1B) potential after the photoexcitation. The major part of the wave-packet decays from S1(1 1B) to S1(2 1A) by the first seam line crossing along the C2-symmetry-breaking directions. The experimentally observed ultrafast S1-S0 decay can be explained by the dynamics through the S1-S0 conical intersection along the direction toward the five-membered ring. The CHD: hexatriene (HT) branching ratio is estimated to be approximately 5:5, which is in accordance with the experiment in solution. This branching ratio is found to be mainly governed by the location of the five-membered ring S1-S0 conical intersection along the ground state potential ridge between CHD and HT.

Journal Article↗
PubMed2006

A crystal structure study when crystallized only in d(CG)3 + methylamine and a d(CG)3 + metal ion.

There is not an example of the crystallization only of d(CG)(3) and a metallic cation without putting the amine in addition in there is no example of the crystallization d(CG)(3) with methylamine that is the mono-amine so far either. We were able to obtain a very beautiful crystal with all sides of 0.3mm by the sitting drop method that had done the crystallization of d(CG)(3)+ methylamine and d(CG)(3)+ Mg(2 +). The crystal was diffracted up to 1.0 A by using the synchrotron radiation. As a result of the X-ray crystal structure analysis, methylamine was not seen while d(CG)(3)+ methylamine was crystallizing mysteriously. d(CG)(3) had stabilized with five Mg(2+) ions. d(CG)(3) had stabilized similarly with five Mg(2+) ions in the crystal of d(CG)(3)+ Mg(2+). The position of these five Mg(2+) ions understood that I agreed on superimpose in a crystal of d(CG)(3) + methylamine, a crystal of d(CG)(3)+Mg(2+), a crystal of d(CG)(3) + spermidine, and crystals of d(CG)(3) + PA (24) which was already analyzed so as to cut it and stabilized d(CG)(3) at an about the same position.

Cations↗
PubMed2006

Structural scaffold of 18-crown-6 tetracarboxylic Acid for optical resolution of chiral amino acid: x-ray crystal analyses of complexes of D- and L-isomers of serine and glutamic acid.

(+)-18-crown-6 tetracarboxylic acid (18C6H4) has been used as a chiral selector for D/L-amino acids in HPLC, where L-isomer is usually eluted prior to D-isomer, except for the case of serine. To clarify why serine exhibits the reverse order for the elusion, the chiral interactions of D- and L-serines with (+)-18C6H4 were investigated by the X-ray single crystal analyses, together with the case of D- and L-glutamic acids, which exhibit the usual elution order in HPLC. The backbone structures (amino, Calpha-H and carboxyl groups) of these four amino acids showed the nearly same interaction with (+)-18C6H4 despite their different chirality. In contrast, the hydroxyl group of L-serine side chain formed a hydrogen bond with the carboxyl group of (+)-18C6H4, whereas such a interaction was not formed for the side chain of D-serine and D- and L-glutamic acids. Thus, it was shown that the exception of D/L-serine from the first elution rule of L-isomer in HPLC is due to the presence and absence of a hydrogen bond formation of its side chain OH group.

Amino Acids↗
PubMed2006

Enantioselective synthesis of a phenylalanine library containing alkyl groups on the aromatic moiety: confirmation of stereostructure by X-ray analysis.

Six phenylalanine analogues containing 2'-methyl-, 2',6'-dimethyl-, 2'-ethyl-6'-methyl-, 2'-isopropyl-6'-methyl-, 2',4',6'-trimethyl-, and 3',5'-dimethyl-L-phenylalanine were synthesized enantioselectively through asymmetric hydrogenation of acetamidoacrylate derivatives. Enzymatic digestion and X-ray analysis supported the L-configuration of the phenylalanine derivatives obtained.

Alkylation↗
PubMed2005

Aromaticity of planar boron clusters confirmed.

Low-energy boron clusters are characterized by two-dimensional geometry. Aromaticity of these planar boron clusters was established in terms of topological resonance energy (TRE). All planar boron clusters were found to be highly aromatic with large positive TREs even if they have 4n pi-electrons. Aromaticity must therefore be the origin of unusual planar or quasi-planar geometry. Thus, the aromaticity concept is as useful in boron chemistry as it is in general organic chemistry. It is evident that the Hückel 4n + 2 rule of aromaticity should not be applied to such polycyclic pi-systems. Some of the boron clusters are in the triplet electronic state to attain higher aromaticity. Multivalency and electron deficiency of boron atoms are responsible for lowering the energies of low-lying pi molecular orbitals and then for enhancing aromaticity. For polycyclic pi-systems, paratropicity does not always indicate antiaromaticity.

Boron↗
PubMed2005

Structural basis for mRNA Cap-Binding regulation of eukaryotic initiation factor 4E by 4E-binding protein, studied by spectroscopic, X-ray crystal structural, and molecular dynamics simulation methods.

Taking advantage of the Trp73 residue located close to the 4E-BP binding site of eIF4E, the interaction between the 4E-BP isoform and eIF4E was investigated by the Trp fluorescence titration method. Although no significant difference was observed among the association constants of three 4E-BP isoforms, the binding preference of 4E-BP2 over 4E-BP1 and -BP3 was shown, probably due to the effect of a 4E-BP2-specific LDRR (60-63) sequence for the binding with eIF4E. By contrast, surface plasmon resonance (SPR) analyses showed the binding preference of 4E-BP1, although the difference among the isoforms was also not significant. This inconsistency with fluorescence analysis likely resulted from the different observation points of the interaction, i.e., local and overall interactions observed by the fluorescence and SPR methods, respectively. To clarify the structural basis for these spectroscopic results, the crystal structure of the ternary complex of m7GpppA-eIF4E-4E-BP1 fragment (Thr36-Thr70) was analyzed by the X-ray diffraction method. Crystal structure analysis at 2.1 A resolution revealed that the 4E-BP1 fragment, assigned to the Pro47-Pro66 peptide moiety, adopted a reverse L-shaped conformation involving the beta sheet and alpha-helical structures and was located at the root of the handle of the temple-bell-shaped eIF4E through hydrophilic and hydrophobic interactions. Based on the observed binding mode, possible interactions with the three 4E-BP isoforms have been discussed. On the other hand, since the crystal structural comparison with the previously determined m7GpppA-eIF4E-4E binary complex showed that the docking of the 4E-BP1 fragment does not significantly affect the overall tertiary structure and cap-binding scaffold of eIF4E, the dynamic regulation of the cap-binding of eIF4E by 4E-BP1 was investigated by molecular dynamics (MD) simulations. Consequently, the simulation suggested that (i) the helical region of the 4E-BP1 peptide is important for the binding with eIF4E, (ii) the existence of a cap structure stabilizes the binding of eIF4E with 4E-BP, (iii) the binding of 4E-BP stabilizes the cap-binding pocket of eIF4E, and (iv) the phosphorylation of Ser67 alone does not induce the separation of 4E-BP from eIF4E, but increases the structural rigidity of 4E-BP. These results provide the structural basis for the mRNA cap-binding regulation of eIF4E by 4E-BP.

Adaptor Proteins, Signal Transducing↗
PubMed2005

Importance of local structures of second and third repeat fragments of microtubule-binding domain for tau filament formation.

To investigate the importance of the seventh residue of the second and third repeat fragments (R2 and R3 peptides) of the microtubule-binding domain (MBD) for tau filamentous assembly, the residues Lys and Pro were substituted (R2-K7P and R3-P7K). The filament formations of the R2 and R3 peptides were almost lost due to their substitutions despite their overall conformational similarities. The NOE analyses showed the importance of the conformational flexibility for the R2 peptide and the coupled extended and helical conformations for the R3 peptide in their limited N-terminal regions around their seventh residues. The result shows that the filament formation of MBD is initiated from a short fragment region containing the minimal conformational or functional motif.

Amino Acid Sequence↗
PubMed2005

Cell adhesion inhibitory activity of (d)-corynoline, a hexahydrobenzo[c]phenanthridine-type alkaloid, and its structure-activity relationship, studied by X-ray crystal structure analysis and molecular docking study.

Corynoline (1), a hexahydrobenzo[c]phenanthridine-type alkaloid, exhibited the concentration-dependent inhibition for the adhesion of human polymorphonuclear leukocyte and eosinophil to human umbilical vein cultured endothelial cell in the concentration range of showing no significant cytotoxicity for the cell: IC(50) value=72.4 microM for (d)-1 and 156.7 microM for (l)-1. This shows the potent anti-inflammatory and/or immunosuppressive activity of 1. To elucidate possible structure-activity relationship, the conformational/structural feature of (d)-1 was investigated by X-ray crystal structure analysis and molecular orbital energy calculations, and the docking study was performed for its interaction with the D1-domain of ICAM-1 (intracellular adhesion molecule-1). A plausible model was proposed, in which all polar atoms of (d)-1 are linked by hydrogen bonds or electrostatic interactions with the functional residues of ICAM-1, that have been supposed to be necessary for the binding with LFA-1 (leukocyte function-associated antigen-1). This suggests the potent inhibitory activity of 1 for the ICAM-1/LFA-1 adhesion and would be important on developing the clinically usable drugs for the inflammatory diseases.

Berberine Alkaloids↗
PubMed2005

Effects of different anti-tau antibodies on tau fibrillogenesis: RTA-1 and RTA-2 counteract tau aggregation.

Tau is the major antigenic component of neurofibrillary pathology in tauopathy, including Alzheimer's disease. Although conversion of soluble tau to an insoluble polymerized fibrillar form is a key factor in the pathogenesis of tauopathy, the mechanism of the change is unclear and no inhibitors of fibril formation are available. Monoclonal antibodies against the 1st or 2nd repeat of the microtubule binding domain, but not the C-terminal 16 residues, completely inhibited tau aggregation into PHF. Furthermore, they did not inhibit tau-induced tubulin assembly. Thus, they are useful to investigate tau protein conversion and will be useful therapeutic lead materials.

Amino Acid Sequence↗