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Y Arata

Publications and source records attributed to Y Arata.

At least 55 records · Page 3Linked to original sources
PubMed1997

Crystallization and preliminary X-ray diffraction studies of a novel killer toxin from a halotolerant yeast Pichia farinosa.

A killer toxin from a halotolerant yeast, Pichia farinosa strain KK1, was crystallized at high- and low-salt concentrations. Crystals from the high-salt solution belonged to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell dimensions of a = b = 81.10, c = 118.46 A. The low-salt solution provided crystals that belonged to the same space group, with nearly same cell dimensions. Preliminary diffraction studies showed that the intensity distributions are significantly different between the two crystals. Both types of crystals contained either two or three molecules per asymmetric unit. They diffracted X-rays beyond 2.0 A resolution and were stable to X-ray irradiation.

Journal Article↗
PubMed1997

Optimization of the water-PRESS pulse sequence and its integration into pulse sequences for studying biological macromolecules.

In this paper, the recently developed "Water-PRESS" method of water suppression [W. .S. Price and Y. Arata (1996), J. Magn. Reson. B 112, 190] in which homospoil pulses are used to manipulate the effects of radiation damping on the water resonance and thereby selectively alter the effective relaxation times of the water resonance with respect to the solute (e.g., biological macromolecules) resonances is further developed and applied. In the present work, methods for optimization in terms of degree of water suppression and in temporal terms (important for the application of Water-PRESS to multidimensional experiments) are considered so that recycle delays of less than 2.3 s (including the acquisition time) are possible. Also, a simple modification which allows the observation of solute resonances with relaxation times similar to that of the water resonance is presented. Finally, the inclusion into more complicated pulse sequences is also discussed. Experimental examples using aqueous samples of lysozyme and immunoglobulin are given. Compared to most other NMR water suppression techniques, this method is extremely simple to implement and optimize and does not require accurately calibrated RF pulses or perfect lineshape.

Animals↗
PubMed1997

The two lectin domains of the tandem-repeat 32-kDa galectin of the nematode Caenorhabditis elegans have different binding properties. Studies with recombinant protein.

Some properties of recombinant proteins derived from the 32-kDa galectin isolated from the nematode Caenorhabditis elegans, which lectin is composed of two tandemly repeated homologous domains [Hirabayashi et al. (1992) J. Biol. Chem. 267, 15485], were studied in order to elucidate the function of this unique polypeptide architecture. We expressed the whole molecule (N32), the N-terminal lectin domain (Nh), and the C-terminal lectin domain (Ch) in Escherichia coli using the expression vector pET21a. All of the recombinant proteins were bound by asialofetuin-Sepharose. CD spectra of the recombinant proteins indicated all of them to be rich in beta-structure and properly refolded. Gel filtration on an HPLC column suggested that all of them existed as monomers. Neither Nh nor Ch seemed to form dimers, in contrast to vertebrate proto-type galectins. Only N32 showed hemagglutination activity towards trypsinized rabbit erythrocytes. Comparison of the affinity of N32, Nh, and Ch for asialofetuin-Sepharose by frontal affinity chromatography [Kasai et al. (1986) J. Chromatogr. 376, 33] showed that Ch has 7-fold weaker affinity than N32, and Nh proved to have still weaker affinity. Since the Asn residue in the CRD (carbohydrate recognition domain), which is conserved in all other galectins, is substituted by Ser in the case of Nh, these data suggest that the two CRDs in this tandem-repeat galectin have different sugar binding properties and that the 32-kDa galectin may serve as a heterobifunctional crosslinker.

Animals↗
PubMed1997

Circular dichroism analysis of the interaction between the alpha and beta subunits in a killer toxin produced by a halotolerant yeast, Pichia farinosa.

SMK toxin is a killer toxin produced by a halotolerant yeast, Pichia farinosa. It is a heterodimer consisting of alpha (63 aa) and beta (77 aa) subunits, between which no disulfide bond exists. The two subunits interact tightly with each other below pH 5. However, the subunits dissociate under neutral conditions, resulting in the aggregation of the alpha subunit and the concomitant loss of killer activity. CD spectral measurements showed that the secondary structure of the SMK toxin changes drastically in the pH range 5.1-5.5 and that after the dissociation of the subunits, the soluble beta subunit alone cannot take any secondary structure. It was also shown that the concentration of NaCl does not affect the secondary structure of the SMK toxin.

Binding Sites↗
PubMed1997

A hidden immunoglobulin G2 in patients with rheumatoid arthritis detected by nuclear magnetic resonance.

OBJECTIVE: The ratios of immunoglobulin (Ig) G1 and IgG2 in patients with rheumatoid arthritis (RA) were examined by nuclear magnetic resonance (NMR) and the results were compared to data obtained by ELISA. METHODS: The IgG of 11 patients with RA were prepared with a DE-52 column and the specific signals for IgG1 and IgG2 were measured by NMR. The ratios of IgG1 and IgG2 were determined by the intensity of this signal. The samples were also measured by ELISA. RESULTS: The ratios of IgG2 in patients with RA measured by NMR were increased significantly compared to controls. However, there were no significant differences in the data determined by ELISA. Thus, a discrepancy exists in the analysis of IgG2 ratios between NMR and ELISA methods. CONCLUSION: There was a discrepancy in the IgG2 ratios of patients with RA between NMR and ELISA methods, and we attribute this to a conformational difference in IgG2 in patients with RA.

Adult↗
PubMed1996

The carbohydrate moiety of the bermuda grass antigen BG60. New oligosaccharides of plant origin.

BG60 is an important allergen of Bermuda grass (Cynodon dactylon) pollen, which causes allergic responses in human. It was suggested that its carbohydrate moiety may be relevant to allergic reaction (Su, S. N., Lau, G. X., Shu, P., Yang, S. Y., Huang, S. W., and Lee, Y. C. (1996) J. Allergy Clin. Immunol., in press). Therefore, the structure of the carbohydrate moiety in BG60 was investigated. The N-linked oligosaccharides were released from the glycopeptides of BG60 by digesting with a glycoamidase from sweet almond and reductively aminated with a fluorescent reagent, 2-aminopyridine. The mixture of pyridylaminated oligosaccharides were separated by high-performance liquid chromatography (HPLC) using an octadecylsilyl (ODS) column. Five oligosaccharide fractions were isolated, and each fraction was found to be homogeneous by HPLC on an amide-silica column. The structure of each of the oligosaccharides was analyzed by the two-dimensional mapping technique (Tomiya, N., Awaya, J., Kurono, M., Endo, S., Arata, Y., and Takahashi, N. (1988) Anal. Biochem. 171, 73-90), in tandem with sequential exoglycosidase digestion. The two most abundant oligosaccharides, A and B, have an unusual structural feature, i.e. the presence of an L-Fuc alpha-(1,3)-linked to Asn-linked GlcNAc without a Xyl beta-(1,2)-linked to the branching Man (see below). To the best of our knowledge, these are the first such oligosaccharides found in plant glycoproteins.

Allergens↗
PubMed1996

Folding topologies of human interleukin-6 and its mutants as studied by NMR spectroscopy.

To understand the structure-function relationship in the human interleukin-6 (IL-6) system, comparative studies were performed on the basis of NMR data obtained using the wild-type IL-6 and six mutants. In each of the six mutants, either Leu152, Leu159, Leu166, Leu168, Leu175, or Leu182, which exist in the C-terminal receptor-binding region, was substituted with Val. The resonance assignments of Val, Ile, Leu, and Phe residues were made by using specific double-labeling and site-specific mutagenesis strategies. On the basis of chemical shift and NOE data collected for six IL-6 mutants and those for the wild-type IL-6, we analyzed the structural changes induced by the substitution of each of the six Leu residues. The NMR data showed that substitution of Leu182 with Val (L182V) induced no structural change in IL-6, suggesting that Leu182 is located on the surface of the IL-6 molecule. A significant decrease in receptor-binding activity was observed in the L182V mutant. It was concluded that the side chain of Leu182 is directly involved in receptor binding. Substitution of Leu175 with Val (L175V) was shown to induce a significant structural change in IL-6. The NMR data are discussed on the basis of the location of four helix elements and an up-up-down-down helix topology of the predicted structure of IL-6 [Bazan, J.F. (1991) Neuron 7, 197-208]. It is possible that helix D bent more sharply toward helix B in the L175V mutant than in the wild-type IL-6 to maintain a closely packed and solvent-inaccessible core formed in the mutated region. It is suggested that the kink of helix D is related to the decrease in receptor-binding activity in the L175V mutant. On the basis of the observed NOE network, the folding topology of IL-6 was analyzed. A comparison of the folding topology of IL-6 with that of human granulocyte colony-stimulating factor determined by X-ray crystallography [Hill, C. P., Osslund, T. D., & Eisenberg, D. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 5167-5171] indicated that IL-6 has a significant similarity of folding topology to that of human granulocyte colony-stimulating factor.

Amino Acid Sequence↗
PubMed1996

Study of urinary mandelic acid concentration and peripheral nerve conduction among styrene workers.

The relationship between exposure to styrene and nerve conduction velocities was investigated in 32 workers occupationally exposed to styrene. There was a dose-dependent relationship between urinary mandelic acid and ulnar and peroneal motor distal latencies (MDLs). The ulnar and peroneal MDLs of subgroup B (urinary mandelic acid > or = 250 mg/l) were significantly longer than those of subgroup A (urinary mandelic acid < 250 mg/l)(p < 0.05), and the referent group (p < 0.03). After adjusting confounding factors, urinary mandelic acid had a significant positive relationship with ulnar and peroneal MDL. Our study suggests that a low level of styrene, below the 50 ppm exposure limit of the American Conference of Governmental Industrial Hygienists (ACGIH), involves the risk of inducing adverse effects on the peripheral nervous system. The study also indicated that motor distal latency is a sensitive parameter of toxic peripheral neuropathy.

Action Potentials↗
PubMed1996

An immunohistochemical study of the 32-kDa galectin (beta-galactoside-binding lectin) in the nematode Caenorhabditis elegans.

The localization of the 32-kDa galectin (beta-galactoside-binding lectin) of the nematode Caenorhabditis elegans, which is the first lectin to be found in a nematode, was examined immunohistochemically using an anti-lectin antiserum. The lectin was found to be localized most abundantly in the adult cuticle and also in the terminal bulb of the pharynx. However, it was difficult to locate the galectin in larval animals, though immunochemical experiments suggested its presence. These results suggest that one of the fundamental roles of the galectin may be as a component of the durable outer barrier, as in the case of the morphogenesis of chick embryonic skin.

Animals↗
PubMed1996

[Effects of age and skin temperature on peripheral nerve conduction velocity--a basic study for nerve conduction velocity measurement in worksite].

The purpose of this study was to investigate the relation between nerve conduction velocity (NCV) and some factors which affect the measurement, such as age, skin temperature, body build and alcohol consumption. Neurophysiological parameters of healthy volunteers (28 males and 27 females, aged 20-57 years) who were free from occupational exposure inducing neuropathy were determined by monitoring skin temperature. A questionnaire survey on height, alcohol and tobacco consumption was also performed. The following results were obtained: 1) Analysis of covariance to examine the relation between age groups and NCVs adjusting for skin temperature showed significant differences only in peroneal motor distal latency (MDL) and duration of sural sensory nerve action potential (SNAP) between age groups. However, there was no constant relation between these parameters and age. Multiple regression analysis showed the significant relationships between age and ulnar MDL and the duration of sural sensory nerve action potential, adjusting for sex, height, weight, BMI, alcohol intake (frequency/week, ethanol equivalent ml/week), tobacco consumption (/day), skin temperature and education years. 2) The skin temperature had significant effects on ulnar MDL, ulnar sensory NCV, duration of ulnar SNAP, sural sensory NCV and amplitude and duration of sural SNAP according to the results of multiple regression analysis and analysis of variance. 3) The body mass index had an independent effect on the ulnar nerve conduction, shortening MDL and the duration of the sensory nerve action potential. 4) Consumption of alcohol and tobacco had no significant relation to nerve conduction velocity in our study. These results show that skin temperature is a major covariate of peripheral nerve conduction and that it is very important to control skin temperature in studies on nerve conduction measurements.

Adult↗
PubMed1995

Three-dimensional structures of the Fab fragment of murine N1G9 antibody from the primary immune response and of its complex with (4-hydroxy-3-nitrophenyl)acetate.

The three-dimensional structures of the Fab fragment, in its unliganded and liganded crystals, of mouse anti-(4-hydroxy-3-nitrophenyl)acetate (NP) antibody N1G9 have been determined by the molecular replacement method. The unliganded and NP-liganded structures were refined at 2.4 A resolution to crystallographic R-factors of 0.194 and 0.196, respectively. Antibody N1G9 bears lambda light chains, and is one of the primary immune response antibodies. Fab N1G9 exhibits an elbow angle of 197 degrees in both structures. This large angle is ascribed to the VL-CL interface formed by lambda-chain residues. A hydrophobic pocket surrounded by the complementarity-determining regions except L2 is identified as a hapten-binding site. Between the liganded and unliganded structures, root-mean-square (r.m.s.) positional deviations are 0.42 A for the main-chain atoms, and 0.74 A for all the protein atoms. The major structural differences between these structures are localized in the hapten-binding site, and yield an r.m.s. deviation of 1.03 A for the side-chain atoms. The soaked NP ligand is in van der Waals contact with the aromatic side-chains of Tyr32L and Trp91L of the light chain, and Trp33H and Tyr97H of the heavy chain, and is hydrogen-bonded to the side-chains of Trp96L, His35H, Arg50H, Tyr95H, and Ser100aH. The side-chain of Lys58H is salt-bridged to the NP hydroxyl group. The side-chains of Arg50H, Trp33H, and Tyr97H are shifted toward the NP carboxyl group. The side-chain of Trp33H, whose replacement to Leu increases affinity by tenfold, is sandwiched between the Arg50H and Tyr97H side-chains, and is in cramped contact both with the ligand and with these side-chains. Affinity increases in the maturation of the anti-NP antibodies are ascribable to conformational relief of these cramped contacts through the replacement of Trp33H or through suitable structural alterations in the H3 region.

Animals↗
PubMed1995

The affinity maturation of anti-4-hydroxy-3-nitrophenylacetyl mouse monoclonal antibody. A calorimetric study of the antigen-antibody interaction.

To understand the mechanism of affinity maturation, we examined the antigen-antibody interactions between 4-hydroxy-3-nitrophenylacetyl (NP) caproic acid and the Fab fragments of three anti-NP antibodies, N1G9, 3B44, and 3B62, by isothermal titration calorimetry. The analyses have revealed that all of these interactions are mainly driven by negative changes in enthalpy. The enthalpy changes decreased linearly with temperature in the range of 25-45 degrees C, producing negative changes in heat capacity. On the basis of the dependence of binding constants on the sodium chloride concentration, we have shown that, during the affinity maturation of the anti-NP antibody, the electrostatic effect does not significantly contribute to the increase in the binding affinity. We have found that, as the logarithm of the binding constants increases during the affinity maturation of the anti-NP antibody, the magnitudes of the corresponding enthalpy, heat capacity, and unitary entropy changes increase almost linearly. On the basis of this correlation, we have concluded that, during the affinity maturation of the anti-NP antibody, a better surface complementarity is attained in the specific complex in order to obtain a higher binding affinity.

Animals↗
PubMed1995

Three-dimensional solution structure of the calcium channel antagonist omega-agatoxin IVA: consensus molecular folding of calcium channel blockers.

The three-dimensional solution structure of omega-agatoxin IVA, which is a specific blocker of the P-type calcium channel isolated from funnel web spider venom and has a molecular mass of 5.2 kDa, was determined by two dimensional 1H NMR spectroscopy, combined with simulated annealing calculations. On the basis of 563 experimental constraints, including 516 distance constraints obtained from the nuclear Overhauser effect, 21 torsion angle (phi, chi 1) constraints, and 26 constraints associated with hydrogen bonds and disulfide bonds, a total of 14 converged structures were obtained. The atomic root mean square difference for the 14 converged structures with respect to the mean coordinates is 0.42 (+/- 0.07) A for the backbone atoms (N, C alpha, C) and 0.95 (+/- 0.15) A for all heavy atoms of the central part (residues 4 to 38) constrained by four disulfide bonds. The N- and C-terminal segments (residues 1 to 3 and 39 to 48, respectively) have a disordered structure in aqueous solution. The molecular structure of omega-agatoxin IVA is composed of a short triple-stranded antiparallel beta-sheet, three loops, and the disordered N- and C-terminal segments. The overall beta-sheet topology is +2x, -1, which is the same as that reported for omega-conotoxin GVIA, an N-type calcium channel blocker. Irrespective of differences in the number of disulfide bonds and low primary sequence homology, these two peptide toxins show a significant structural similarity in three dimensions. The whole-cell voltage-clamp recording using rat cerebellar slices suggests that the hydrophobic C-terminal segment of omega-agatoxin IVA, which does not exist in omega-conotoxin GVIA, plays a crucial role in the blocking action of omega-agatoxin IVA on the P-type calcium channel in rat cerebellar Purkinje cells. The present study provides a molecular basis for the toxin-channel interaction, and thereby provides insight into the discrimination of different subtypes of calcium channels.

Amino Acid Sequence↗
PubMed1995

Proteolytic fragmentation with high specificity of mouse immunoglobulin G. Mapping of proteolytic cleavage sites in the hinge region.

We report the results of fragmentation of mouse IgG by clostripain, lysyl endopeptidase, metalloendopeptidase, and V8 protease that have a narrower substrate specificity than papain and pepsin. A panel of mouse monoclonal switch variant antibodies with IgG1, IgG2a, and IgG2b subclasses were examined. Cleavage sites by these proteases were mapped on the hinge region of each of the IgG subclasses. It was demonstrated that lysyl endopeptidase can cleave the core hinge portion of IgG2a and IgG2b without perturbing the inter-chain disulfide bridges. Digestion products were successfully isolated by a combined use of protein A affinity chromatography and HPLC techniques. This is a first successful attempt of obtaining the F(ab')2 fragment of IgG2b by proteolytic digestion.

Alkylation↗
PubMed1995

Identification of neutral and sialyl N-linked oligosaccharide structures from human serum glycoproteins using three kinds of high-performance liquid chromatography.

The distribution of neutral and sialyl N-linked oligosaccharides from human serum glycoproteins has been studied using three kinds of HPLC columns as described below. N-linked oligosaccharides were released from chymotrypsin- and trypsin-digested glycopeptides of human serum by means of glycoamidase (from almond) digestion. The reducing ends of the oligosaccharides were derivatized with the fluorescent reagent 2-aminopyridine (PA). The mixture of PA-oligosaccharides was separated by high-performance liquid chromatography on a diethylaminoethyl column according to the sialic acid content. Each fraction separated was then applied on an octadecylsilyl (ODS) column, and the elution volume of each peak was recorded as a glucose unit on the X-axis. Then, each of the separated oligosaccharides was applied to the amide column. Each peak's elution volume was recorded as a glucose unit on the Y-axis. The elution volumes from these two columns (ODS and amide) provide a unique set of coordinates. The structure of each sialyl oligosaccharide fraction was analyzed by the same two-dimensional sugar-mapping technique as previously developed for neutral oligosaccharides. This was combined with exoglycosidase digestion and high-resolution proton NMR measurement. Fourteen neutral, eight mon-sialyl, four di-sialyl, and five tri-sialyl oligosaccharides were isolated from human serum and their structures were characterized.

Amidohydrolases↗
PubMed1995

Comparative thermodynamic analyses of the Fv, Fab* and Fab fragments of anti-dansyl mouse monoclonal antibody.

In order to investigate the role of the constant domains on the antigen-binding property of the variable domains, we have carried out a comparative thermodynamic study of the anti-dansyl Fv, Fab* and Fab fragments that possess the identical amino acid sequence of the variable domains. The thermodynamic analyses have shown that binding constants, enthalpy changes and entropy changes are similar for the three antigen-binding fragments, whereas the thermal stability of Fab is much higher than that of Fv and Fab*. We have concluded that (i) the variable domains of the three antigen-binding fragments possess identical intrinsic capability for antigen binding and (ii) the two constant domains serve to improve the stability of the variable domains.

Animals↗