Biomedical subjects

Takao Sato

Publications and source records attributed to Takao Sato.

At least 19 recordsLinked to original sources

PubMed2006

Reversed Café Wall illusion with missing fundamental gratings.

The direction of Café Wall illusion was measured for ordinary Café Wall figures comprised of blocks with a square wave profile and for those with a missing fundamental (MF) profile. For the MF version, it was found that the illusion direction alternates according to the patterns' main component frequency when the shift between adjacent rows was systematically varied. The direction of illusion for the MF version was opposite to that for the original version when the phase shifts of adjacent rows were between 60 and 120degrees of the original grating. The results indicate that the illusion depends on the physical component rather than the appearance of the pattern. The possibility of the Café Wall illusion being mediated by low-level luminance mechanisms each tuned to a different spatial frequency is discussed based on the results.

Humans↗

PubMed2006

The interaction and compatibility between a soft contact lens and an ophthalmic drug.

PURPOSE: To investigate the interaction and compatibility between a soft contact lens (SCL) and an ophthalmic drug. METHODS: Samples were prepared with the nonionic SCL (groups I and II), the anionic SCL (group IV), and the zwitter ionic SCL (group IV). Chlorpheniramine maleate and sodium cromoglycate were used to measure the drug uptake into the SCL. RESULTS: The results showed the largest drug uptake into the anionic SCL accompanied with dimensional changes and lower drug uptakes into the nonionic and the zwitter ionic SCL with dimensional stability. The cell permeability of the substances when instilled in the eye over the SCL was also measured. The zwitter ionic SCL allowed cell permeability comparable to that by oral administration. CONCLUSIONS: These results indicated the possibility for the zwitter ionic SCL as a lens to be worn concomitantly with ophthalmic drug instillation.

Animals↗

PubMed2006

Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes.

Human rck/p54, a product of the gene cloned at the breakpoint of t(11; 14) (q23;q32) chromosomal translocation on 11q23 in B-cell lymphoma, is a member of the DEAD-box RNA helicase family. Here, the crystal structure of Nc-rck/p54, the N-terminal core domain of rck/p54, revealed that the P-loop in motif I formed a closed conformation, which was induced by Asn131, a residue unique to the RCK subfamily. It appears that ATP does not bind to the P-loop. The results of dynamic light scattering revealed to ATP-induced conformational change of rck/p54. It was demonstrated that free rck/p54 is a distended molecule in solution, and that the approach between N-terminal core and C-terminal domains for ATP binding would be essential when unwinding RNA. The results from helicase assay using electron micrograph, ATP hydrolytic and luciferase assay showed that c-myc IRES RNA, whose secondary structure regulates IRES-dependant translation, was unwound by rck/p54 and indicated that it is a good substrate for rck/p54. Over-expression of rck/p54 in HeLa cells caused growth inhibition and cell cycle arrest at G2/M with down-regulation of c-myc expression. These findings altogether suggest that rck/p54 may affect the IRES-dependent translation of c-myc even in the cells.

Adenosine Triphosphate↗

PubMed2006

[A case of myasthenia gravis appearing after thymomectomy: with histopathological investigation].

We report a 64-years old man who had myasthenia gravis (MG) appearing after surgical removal of thymoma. His thymoma was not removed completely due to adhesion with other organs. Histopathologicaly, the thymoma was an invasive and predominantly epithelial type. CD45RO positive cells increased in the thymus. After five months of thymectomy, he received radiation therapy because the remaining tumor grew up slightly. The radiation was effective, and the recurrence of tumor has never been detected after that. However, nine months after the surgery, he noticed ptosis and double vision, and he was diagnosed as MG because of positive serum anti-AchR antibody and positive Tensilon test. He received oral prednisolone, and he has kept a good condition. Previous reports have shown that an extensive thymectomy tends to reduce the incidence of post-operative MG. In our case, the remaining thymoma might increase the risk of MG. And the removed thymus might contain an unknown regulatory factor that could inhibit a development of MG. The risk factor for development of post-operative MG should be investigated in future.

Anti-Inflammatory Agents↗

PubMed2005

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.

Bacterial Proteins↗

PubMed2005

Backscroll illusion: apparent motion in the background of locomotive objects.

Backscroll illusion is an apparent motion perceived in backgrounds of movie images that present locomotive objects such as people, animals, and vehicles. This illusion is from the visual system registering retinal motion signals in relation to high-level object motion signals. We confirmed this notion from psychophysical experiments that mainly presented a realistic human figure on a treadmill walking or running in front of a counterphase grating. The apparent grating motion was consistently induced in the direction opposite to the locomotion. The induction was tuned to a gait velocity. The time course showed that the illusion arose as if it was synchronized with gait recognition, and that it was sustained against several reversals of limb swings so that local motion accounts were denied. A weak but significant illusion was observed from a static figure that implied a gait. Thus, we concluded that the illusion was determined by the high-level recognition of biological motion. An additional experiment found a similar effect from a vehicle with rotating wheels but no induction from a rotating wheel per se. This result led us to hypothesize that the backscroll illusion is generalized to objects that have shapes implying their moving directions.

Adult↗

PubMed2005

Precipitation diagram and optimization of crystallization conditions at low ionic strength for deglycosylated dye-decolorizing peroxidase from a basidiomycete.

The growth of suitably sized protein crystals is essential for protein structure determination by X-ray crystallography. In general, crystals are grown using a trial-and-error method. However, these methods have been modified with the advent of microlitre dispensing-robot technology and of protocols that rapidly screen for crystal nucleation conditions. The use of one such automatic dispenser for mixing protein drops (1.3-2.0 microl in volume) of known concentration and pH with precipitating solutions (ejecting 2.0 microl droplets) containing salt is described here. The results of the experiments are relevant to a crystallization approach based on a two-step procedure: screening for the crystal nucleation step employing robotics followed by optimization of the crystallization conditions using incomplete factorial experimental design. Large crystals have successfully been obtained using quantities as small as 3.52 mg protein.

Basidiomycota↗

PubMed2005

Crystallization and X-ray analysis of 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics.

A recombinant 2-deoxy-scyllo-inosose synthase from Bacillus circulans has been crystallized at 277 K using PEG 4000 as precipitant. The diffraction pattern of the crystal extends to 2.30 A resolution at 100 K using synchrotron radiation at the Photon Factory. The crystals are monoclinic and belong to space group P2(1), with unit-cell parameters a = 80.5, b = 70.4, c = 83.0 A, beta = 117.8 degrees. The presence of two molecules per asymmetric unit gives a crystal volume per protein weight (VM) of 2.89 A3 Da(-1) and a solvent constant of 57.4% by volume.

Aminoglycosides↗

PubMed2005

Structural consequences of hen egg-white lysozyme orthorhombic crystal growth in a high magnetic field: validation of X-ray diffraction intensity, conformational energy searching and quantitative analysis of B factors and mosaicity.

A novel method has been developed to improve protein-crystal perfection during crystallization in a high magnetic field and structural studies have been undertaken. The three-dimensional structure of orthorhombic hen egg-white (HEW) lysozyme crystals grown in a homogeneous and static magnetic field of 10 T has been determined and refined to a resolution of 1.13 angstroms and an R factor of 17.0%. The 10 T crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.54 (3), b = 73.86 (6), c = 30.50 (2) angstroms and one molecule per asymmetric unit. A comparison of the structures of the 0 T and 10 T crystals has been carried out. The magnitude of the structural changes, with a root-mean-square deviation value of 0.75 angstroms for the positions of all protein atoms, is similar to that observed when an identical protein structure is resolved in two different crystalline lattices. The structures remain similar, with the exception of a few residues e.g. Arg68, Arg73, Arg128 and Gln121. The shifts of the arginine residues result in very significant structural fluctuations, which can have large effects on a protein's crystallization properties. The high magnetic field contributed to an improvement in diffraction intensity by (i) the displacement of the charged side chains of Arg68 and Arg73 in the flexible loop and of Arg128 at the C-terminus and (ii) the removal of the alternate conformations of the charged side chains of Arg21, Lys97 or Arg114. The improvement in crystal perfection might arise from the magnetic effect on molecular orientation without structural change and differences in molecular interactions. X-ray diffraction and molecular-modelling studies of lysozyme crystals grown in a 10 T field have indicated that the field contributes to the stability of the dihedral angle. The average difference in conformational energy has a value of -578 kJ mol(-1) per charged residue in favour of the crystal grown in the magnetic field. For most protein atoms, the average B factor in the 10 T crystal shows an improvement of 1.8 angstroms(2) over that for the 0 T control; subsequently, the difference in diffraction intensity between the 10 T and 0 T crystals corresponds to an increase of 22.6% at the resolution limit. The mosaicity of the 10 T crystal was better than that of the 0 T crystal. More highly isotropic values of 0.0065, 0.0049 and 0.0048 degrees were recorded along the a, b and c axes, respectively. Anisotropic mosaicity analysis indicated that crystal growth is most perfect in the direction that corresponds to the favoured growth direction of the crystal, and that the crystal grown in the magnetic field had domains that were three times the volume of those of the control crystal. Overall, the magnetic field has improved the quality of these crystals and the diffracted intensity has increased significantly with the magnetic field, leading to a higher resolution.

Animals↗

PubMed2005

A norovirus protease structure provides insights into active and substrate binding site integrity.

Norovirus 3C-like proteases are crucial to proteolytic processing of norovirus polyproteins. We determined the crystal structure of the 3C-like protease from Chiba virus, a norovirus, at 2.8-A resolution. An active site including Cys139 and His30 is present, as is a hydrogen bond network that stabilizes the active site conformation. In the oxyanion hole backbone, a structural difference was observed probably upon substrate binding. A peptide substrate/enzyme model shows that several interactions between the two components are critical for substrate binding and that the S1 and S2 sites appropriately accommodate the substrate P1 and P2 residues, respectively. Knowledge of the structure and a previous mutagenesis study allow us to correlate proteolysis and structure.

3C Viral Proteases↗

PubMed2004

Crystallization and preliminary X-ray studies on the reaction center-light-harvesting 1 core complex from Rhodopseudomonas viridis.

The reaction center-light-harvesting 1 (RC-LH1) core complex is the photosynthetic apparatus in the membrane of the purple photosynthetic bacterium Rhodopseudomonas viridis. The RC is surrounded by an LH1 complex that is constituted of oligomers of three types of apoproteins (alpha, beta and gamma chains) with associated bacteriochlorophyll bs and carotenoid. It has been crystallized by the sitting-drop vapour-diffusion method. A promising crystal diffracted to beyond 8.0 A resolution. It belonged to space group P1, with unit-cell parameters a = 141.4, b = 136.9, c = 185.3 A, alpha = 104.6, beta = 94.0, gamma = 110.7 degrees. A Patterson function calculated using data between 15.0 and 8.0 A resolution suggested that the LH1 complex is distributed with quasi-16-fold rotational symmetry around the RC.

Bacterial Proteins↗

PubMed2004

Crystallization and preliminary X-ray crystallographic analysis of chitinase F1 (ChiF1) from the alkaliphilic Nocardiopsis sp. strain F96.

Chitinase F1 (ChiF1) isolated from the alkaliphilic Nocardiopsis sp. strain F96 is a family 18 chitinase that hydrolyzes chitin, an insoluble beta-1,4-linked polymer of N-acetylglucosamine. Crystals of recombinant ChiF1 with molecular weight of 33 000 Da were grown to a suitable size for X-ray structure analysis using 18%(w/v) polyethylene glycol 8000, 200 mM zinc acetate dehydrate and 100 mM sodium cacodylate buffer pH 6.5. Diffraction data were collected at SPring-8 and show that the crystals belong to the trigonal space group P3(1)12 or P3(2)12, with unit-cell parameters a = 56.0, c = 179.5 A, and diffract X-rays beyond 1.2 A resolution. Crystallographic analysis was carried out using the multiwavelength anomalous diffraction (MAD) method using zinc as the anomalous scatter. The binding of Zn atoms was clarified from the Bijvoet and dispersive Patterson functions, which gave prominent zinc-zinc self-vectors on the Harker section.

Actinomycetales↗

PubMed2004

Crystallization and preliminary X-ray diffraction studies of the hyperthermophilic archaeal sulredoxin having the unique Rieske [2Fe-2S] cluster environment.

The hyperthermophilic archaeal sulredoxin from Sulfolobus tokodaii is a water-soluble high-potential Rieske [2Fe-2S] protein with unique pH-dependent redox properties compared with its mesophilic homologues in cytochrome bc1/b6f complexes. The oxidized recombinant sulredoxin has been crystallized by the hanging-drop vapour-diffusion method using 30%(v/v) polyethylene glycol 400, 0.1 M cadmium chloride and 0.1 M sodium acetate pH 4.6. The crystals diffracted to beyond 2.0 A resolution and belong to the cubic space group F4(1)32, with unit-cell parameter a = 163.00 +/- 0.05 A. The asymmetric unit contains one sulredoxin molecule. Three-wavelength MAD data were collected.

Archaeal Proteins↗

PubMed2004

Structure of bovine carbonic anhydrase II at 1.95 A resolution.

Carbonic anhydrase (CA) is a zinc-containing enzyme that catalyzes the reversible hydration of CO2 to HCO3-. In eukaryotes, the enzyme plays a role in various physiological functions, including interconversion between CO2 and HCO3- in intermediary metabolism, facilitated diffusion of CO2, pH homeostasis and ion transport. The structure of bovine carbonic anhydrase II (BCA II) has been determined by molecular replacement and refined to 1.95 A resolution by simulated-annealing and individual B-factor refinement. The final R factor for the BCA II structure was 19.4%. BCA II has a C-terminal knot structure similar to that observed in human CA II. It contains one zinc ion in the active site coordinated to three histidines and one putative water molecule in a tetrahedral geometry. The structure of BCA II reveals a probable alternative proton-wire pathway that differs from that of HCA II.

Animals↗

PubMed2003

Crystallization and X-ray analysis of the N-terminal core domain of a tumour-associated human DEAD-box RNA helicase, rck/p54.

The RCK gene was cloned on the basis of the t(11;14)(q23;q32) chromosome translocation observed in human B-cell lymphoma cell line RC-K8. This gene was found to be overexpressed in various kinds of tumours. The gene product, rck/p54, consisting of 472 amino-acid residues with molecular weight 53.2 kDa, belongs to the family of DEAD-box RNA helicases. Its ATP-dependent RNA-unwinding activity toward c-myc RNA molecules in vitro has recently been demonstrated. In the present study, limited proteolysis experiments of rck/p54 were used to truncate the N-terminal domain (residues 1-288; 31.8 kDa) of rck/p54, leading to successful crystallization of Nc-rck/p54, i.e. the N-terminal core domain (residues 70-288; 24.5 kDa) of rck/p54. Crystals of Nc-rck/p54 were grown to a size suitable for X-ray structure analysis using polyethylene glycol 3350 as the precipitant. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 65.5, b = 73.1, c = 84.8 A, and diffracts X-rays to beyond 2.0 A resolution.

Amino Acid Sequence↗

PubMed2003

A unique dye-decolorizing peroxidase, DyP, from Thanatephorus cucumeris Dec 1: heterologous expression, crystallization and preliminary X-ray analysis.

The dye-decolorizing peroxidase DyP is a key enzyme in the decolorizing fungus Thanatephorus cucumeris Dec 1 that degrades azo and antraquinone dyes. The gene dyp from T. cucumeris Dec 1, which has low homology to other peroxidase genes, was cloned and transformed into Aspergillus oryzae and glycosylated DyP was expressed at high levels. Purified DyP was deglycosylated using GST Endo F1 and then crystallized in a strong magnetic field (10 T) at 283 K using ammonium sulfate as precipitant. X-ray diffraction data to 2.96 A resolution collected from a native crystal at the Photon Factory (Tsukuba, Japan) showed that the crystal belonged to the hexagonal space group P6(5)22, with unit-cell parameters a = b = 136.15, c = 363.46 A. The asymmetric unit of the crystal contained four DyP molecules, with a corresponding Matthews coefficient (V(M)) of 2.50 A(3) Da(-1) and a solvent content of 51%. Heavy-atom derivatives of DyP have been obtained and electron-density maps have been calculated. The haem is visible and continuous electron density between the haem and protein clearly indicates the location of the proximal histidine ligand.

Aspergillus oryzae↗

PubMed2003

Azulene incorporation and release by hydrogel containing methacrylamide propyltrimenthylammonium chloride, and its application to soft contact lens.

We have developed the epoch-making contact lens that is equipped with drug delivery system. The hydrogels contain cationic functional group in its side chain were prepared with 2-hydroxyethyl methacylate (HEMA) and methacrylamide propyltrimethylammonium chloride (MAPTAC). The obtained hydrogel is capable to store the anionic drug such as azulene based on ion-exchange reaction. The incorporated anionic drug would be released in physiological condition. The size change of the hydrogel may occur before and after drug release, but we have discovered that the addition of anionic monomer such as methacrylic acid (MAA) and 2-methacryloxyethyl acid phosphate (MOEP) to the above-mentioned composition is effective to prevent the size change, indicating that this hydrogel has the possibility to be applied as a significant drug delivery system device.

Ammonium Chloride↗

PubMed2003

Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain.

Although some exceptional motifs have been identified, it is well known that the PXXP motif is the motif of ligand proteins generally recognized by the Src homology 3 (SH3) domain. SH3-ligand interactions are usually weak, with ordinary KD approximately 10 microM. The structural basis for a tight and specific association (KD = 0.24 microm) between Gads SH3 and a novel motif, PX(V/I)(D/N)RXXKP, was revealed in a previous structural analysis of the complex formed between them. In this paper, we report the crystal structure of the signal transducing adaptor molecule-2 (STAM2) SH3 domain in complex with a peptide with a novel motif derived from a ligand protein, UBPY. The derived KD value for this complex is 27 microM. The notable difference in affinity for these parallel complexes may be explained because the STAM2 SH3 structure does not provide a specificity pocket for binding, whereas the Gads SH3 structure does. Instead, the structure of STAM2 SH3 is analogous to that of Grb2 SH3 which, in addition to normal PXXP ligands, has also been shown to moderately recognize the novel motif discussed herein. Thus, the extremely tight interaction observed between Gads SH3 and the novel motif is caused not by an innate ability of the novel motif but rather by an evolutionary change in the Gads SH3 domain. Instead, SH3 domains of STAM2 and Grb2 retain the moderate characteristics of recognizing their ligand proteins like other SH3 domains for appropriate transient interactions between signaling molecules.

Adaptor Proteins, Signal Transducing↗