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Biomedical subjects

Y Shimonishi

Publications and source records attributed to Y Shimonishi.

At least 37 records · Page 2Linked to original sources
PubMed1999

Structural characterization of Acetobacter diazotropicus levansucrase by matrix-assisted laser desorption/ionization mass spectrometry: identification of an N-terminal blocking group and a free-thiol cysteine residue.

High-resolution matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to characterize the primary structure of the levansucrase (EC 2.4.1.10) secreted by Acetobacter diazotropicus SRT4. The technique permitted not only the reading frame of this enzyme, the amino acid sequence of which was deduced from DNA, but also the elucidation of an N-terminal blocking group and the position of a disulfide bridge between Cys309 and Cys365 among the three Cys residues. A free cysteine (Cys127) was identified by modifying an intact molecule with a sulfhydryl reagent, 5-(octyldithio)-2-nitrobenzoic acid, under non-reducing conditions. In addition, the enzyme obtained by site-directed mutagenesis at Asp279 to Asn279 was also identified by the above methods. Post-source decay analysis of the tryptic peptide containing the mutation site unequivocally revealed an Asn residue at position 279.

Acetobacter↗
PubMed1999

Expression and characterization of the extracellular domain of guanylyl cyclase C from a baculovirus and Sf21 insect cells.

Guanylyl cyclase (GC)-C, a single-transmembrane receptor protein for heat-stable enterotoxin, guanylin, and uroguanylin, and its N-terminal extracellular domain were prepared at a high level of expression from a system constructed of Sf21 insect cells and recombinant baculovirus. The recombinant GC-C, containing the complete sequence, retained its binding affinity to heat-stable enterotoxin with a KD value (6.2 x 10(-10) M) and cyclase catalytic activity at a level similar to those of GC-C expressed in mammalian cell lines, such as COS-7. The N-terminal extracellular domain was prepared in a form which contained the hexahistidine tail at its C-terminus and was purified as a homogenous protein by Con A and Ni-chelating affinity chromatography from the culture medium of the insect cells. The purified N-terminal extracellular domain of GC-C exhibited the high (KD = 4 x 10(-10) M) and low (KD = 7 x 10(-8) M) affinity sites in binding to heat-stable enterotoxin. These results clearly indicate that the N-terminal extracellular domain of GC-C possesses the same biochemical characteristics as the complete GC-C protein even in the membrane-free form. Moreover, the extracellular domain is able to form an oligomer in a ligand-dependent manner, suggesting that the N-terminal extracellular domains interact with one another in binding to ligands.

Animals↗
PubMed1999

Thallium and FDG uptake by atelectasis with bronchogenic carcinoma.

We report a case of bronchogenic carcinoma with atelectasis studied by T1-SPECT and FDG-PET. In the carcinoma, abnormally high uptake of T1 and FDG were detected, but in the region of atelectasis, an abnormally high uptake of T1 with a relatively low uptake of FDG were observed. On quantitative analyses, the T1 retention indexes of the tumor and atelectasis were 29.7 and 42.0. The mean SUVs of FDG of the tumor and the atelectasis were 8.92 and 1.28. T1-SPECT could not distinguish the atelectasis from the carcinoma. FDG-PET was superior to T1-SPECT in this case in detecting malignancy and distinguishing it from atelectasis.

Biological Transport↗
PubMed1999

Chloroplast Cpn20 forms a tetrameric structure in Arabidopsis thaliana.

Chloroplast chaperonin 20 (Cpn20) in higher plants is a functional homologue of the Escherichia coli GroES, which is a critical regulator of chaperonin-mediated protein folding. The cDNA for a Cpn20 homologue of Arabidopsis thaliana was isolated. It was 958 bp long, encoding a protein of 253 amino acids. The protein was composed of an N-terminal chloroplast transit peptide, and the predicted mature region comprised two distinct GroES domains that showed 42% amino acid identity to each other. The isolated cDNA was constitutively expressed in transgenic tobacco. Immunogold labelling showed that Cpn20 is accumulated in chloroplasts of transgenic tobacco. A Northern blot analysis revealed that mRNA for the chloroplast Cpn20 is abundant in leaves and is increased by heat treatment. To examine the oligomeric structure of Cpn20, a histidine-tagged construct lacking the transit peptide was expressed in E. coli and purified by affinity chromatography. Gel-filtration and cross-linking analyses showed that the expressed products formed a tetramer. The expressed products could substitute for GroES to assist the refolding of citrate synthase under non-permissive conditions. The analysis on the subunit stoichiometry of the GroEL-Cpn20 complex also revealed that the functional complex is composed of a GroEL tetradecamer and a Cpn20 tetramer.

Arabidopsis↗
PubMed1999

The relevance of N-linked glycosylation to the binding of a ligand to guanylate cyclase C.

The role of carbohydrate moieties at the N-linked glycosylation sites of guanylate cyclase C (GC-C), a receptor protein for guanylin, uroguanylin and heat-stable enterotoxin, in ligand binding and structural stability was examined using site-directed mutagenesis of the putative N-linked glycosylation sites in the extracellular domain (ECD) of porcine GC-C. For this purpose, eight mutant proteins of ECD (N9A, N20A, N56A, N172A, N261A, N284A, N334A and N379A) and six mutant proteins of the complete GC-C (N9A, S11A, N172A, T174A, N379A and T381A) were prepared, in which Ala replaced Asn, Ser and Thr at the N-linked glycosylation consensus sites. All the mutant proteins showed a ligand-binding affinity (K(d)) similar to those of the wild-type proteins, although the deletion of a carbohydrate moiety at each of the N-linked glycosylation sites affected the ligand-binding ability of ECD or GC-C to some degree. However, the mutant proteins of ECD (N379A) and GC-C (N379A and T381A) showed considerably decreased binding ability in the context of maximum capacity (B(max)) to a ligand, despite the fact that the expression levels of these mutant proteins were nearly the same as the wild-type proteins. Moreover, the mutant protein of ECD (N379A) was considerably less stable to a denaturant. These results clearly indicate a crucial role for the carbohydrate moiety at N379, which is located near the transmembrane region, in structural stability, the ability to bind to a ligand and the cyclase catalytic activity of GC-C, and provide a route for the elucidation of the mechanism of the interaction between GC-C and a ligand.

Amino Acid Sequence↗
PubMed1999

Complementary DNA cloning and characterization of ferredoxin localized in bundle-sheath cells of maize leaves.

In maize (Zea mays L.) two leaf-specific ferredoxin (Fd) isoproteins, Fd I and Fd II, are distributed differentially in mesophyll and bundle-sheath cells. A novel cDNA encoding the precursor of Fd II (pFD2) was isolated by heterologous hybridization using a cDNA for Fd I (pFD1) as a probe. The assignment of the cDNAs to the Fds was verified by capillary liquid-chromatography/electrospray ionization-mass spectrometry. RNA-blot analysis demonstrated that transcripts for Fd I and Fd II accumulated specifically in mesophyll and bundle-sheath cells, respectively. The mature regions of pFD1 and pFD2 were expressed in Escherichia coli as functional Fds. Fd I and Fd II had similar redox potentials of -423 and -406 mV, respectively, but the Km value of Fd-NADP+ reductase for Fd II was about 3-fold larger than that for Fd I. Asparagine at position 65 of Fd II is a unique residue compared with Fd I and other Fds from various plants, which have aspartic acid or glutamic acid at the corresponding position as an electrostatic interaction site with Fd-NADP+ reductase. Substitution of asparagine-65 with aspartic acid increased the affinity of Fd II with Fd-NADP+ reductase to a level comparable to that of Fd I. These structural and functional differences of Fd I and Fd II may be related to their cell-specific expression in the leaves of a C4 plant.

Amino Acid Sequence↗
PubMed1999

Role of the prosequence of guanylin.

Guanylin is a guanylyl cyclase (GC)-activating peptide that is mainly secreted as the corresponding prohormone of 94 amino acid residues. In this study, we show that the originally isolated 15-residue guanylin, representing the COOH-terminal part of the prohormone, is released from the prohormone by cleavage of an Asp-Pro amide bond under conditions applied during the isolation procedures. Thus, the 15-residue guanylin is probably a non-native, chemically induced GC-activating peptide. This guanylin molecule contains two disulfide bonds that are absolutely necessary for receptor activation. We demonstrate that the folding of the reduced 15-residue guanylin results almost completely in the formation of the two inactive disulfide isomers. In contrast, the reduced form of proguanylin containing the entire prosequence folds to a product with the native cysteine connectivity. Because proguanylin lacking the 31 NH2-terminal residues of the prosequence folds only to a minor extent to guanylin with the native disulfide bonds, it is evident that this NH2-terminal region contributes significantly to the correct disulfide-coupled folding. Structural studies using CD and NMR spectroscopy show that native proguanylin contains a considerable amount of alpha-helical and, to a lesser extent, beta-sheet structural elements. In addition, a close proximity of the NH2- and the COOH-terminal regions was found by NOESY. It appears that this interaction is important for the constitution of the correct conformation and provides an explanation of the minor guanylyl cyclase activity of proguanylin by shielding the bioactive COOH-terminal domain from the receptor.

Amino Acid Sequence↗
PubMed1998

Structural analysis of oligosaccharides derivatized with 4-aminobenzoic acid 2-(diethylamino)ethyl ester by matrix-assisted laser desorption/ionization mass spectrometry.

Oligosaccharides derivatized with 4-aminobenzoic acid 2-(diethylamino) ethyl ester (ABDEAE) can be analyzed by ESI (Yoshino, K.; et al. Anal. Chem. 1995, 67, 4028-4031) and MALDI (Takao, T.; et al. Rapid Commun. Mass Spectrom. 1996, 10, 637-640) mass spectrometry. In this study, oligosaccharides derived from the enzymatic cleavage of the sugar chains of glycoproteins ribonuclease B, erythropoietin, and transferrin were subjected to ABDEAE derivatization, prior to analysis on a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF MS) for high-resolution mass measurement and a postsource decay (PSD) experiment. In the mass measurement of ABDEAE derivatives, quasi-molecular ion species have been observed in monoisotopic resolution using 2,5-dihydroxybenzoic acid as the matrix from spots that contain 50-200 fmol of sample; in the PSD analyses from the spots contained 500 fmol-1 pmol of sample, the predominant backbone ion series which covers the entire mass range for all the derivatives, the internal ion series which reflect the branched trimannosyl core structure of N-glycans, and the low m/z fingerprint ion of ABDEAE were consecutively observed, permitting structure elucidation of the oligosaccharides. Given the effectiveness of this derivatization in terms of its high sensitivity and resolution with respect to MALDI-TOF MS, current methodology is clearly applicable to the sensitive detection and accurate structural analysis of N-glycans.

Carbohydrate Sequence↗
PubMed1998

Specific isoprenyl group linked to transducin gamma-subunit is a determinant of its unique signaling properties among G-proteins.

Among 11 subtypes of heterotrimeric G-protein gamma-subunit, gamma1 (rod), gamma8 (cone) and gamma11 are modified with farnesyl while the others are modified with geranylgeranyl at the C-terminus. To understand the role of specific isoprenylation (farnesylation) of retinal transducin, we examined how and to what extent the type of isoprenyl group affects transducin-beta gamma (beta1 gamma1) functions such as interactions with membranes, Galpha/receptor, and effectors. To this end, the C-terminal farnesylation signal sequence (CVIS) of gamma1 was replaced by a geranylgeranylation signal (CVIL), and the resultant mutant (S74L) or wild-type (WT) gamma1 was coexpressed with beta1 in the baculovirus-Tn5 insect cell system. Both gamma1WT and gamma1S74L expressed as a beta gamma complex were mixtures modified with farnesyl and geranylgeranyl groups. The ratio of farnesyl to geranylgeranyl in preparations of beta1 gamma1WT and beta1 gamma1S74L purified from the Tn5 cell membrane fraction was about 1:2 and 1:6, respectively. These two forms of recombinant beta1 gamma1 and retinal beta1 gamma1 were different in their abilities to associate with rod outer segment membranes with the following rank order: beta1 gamma1S74L > beta1 gamma1WT > retinal beta1 gamma1. Functionally, beta1 gamma1S74L was the most potent to promote pertussis toxin-catalyzed ADP ribosylation of transducin-alpha (Talpha), to stimulate metarhodopsin II-catalyzed GTPgammaS-binding reaction to Talpha and to modulate adenylyl cyclase and phospholipase C activities. All of the beta1 gamma1 functions absolutely required the isoprenylation of the gamma-subunit. As for the interaction with Goalpha and adenylyl cyclase, predominantly geranylgeranylated beta1 gamma1S74L was less effective than geranylgeranylated beta1 gamma2 purified from bovine brain. These results demonstrate that the properties of Gbeta gamma are strongly affected by the type of functionally indispensable isoprenylation in addition to the amino acid sequence of Ggamma. The relative contribution of the two factors depends on proteins with which Gbeta gamma interacts.

Animals↗
PubMed1998

In vitro disulfide-coupled folding of guanylyl cyclase-activating peptide and its precursor protein.

Guanylyl cyclase-activating peptide II (GCAP-II), an endogenous ligand of particulate guanylyl cyclase C (GC-C), is processed from the precursor protein and circulates in human blood. GCAP-II consists of 24 amino acid residues and contains two disulfide bridges. The correct disulfide paring of GCAP-II is an absolute requirement for its biological activity. This study shows that the folding of the peptide from the reduced form yields a peptide with the native disulfide paring as a minor product and with non-native ones as major products, regardless of the presence or absence of reduced and oxidized glutathione. The results suggest that GCAP-II does not possess sufficient information to permit the adoption of the native conformation and to effectively form the correct disulfide pairing and, as a result, that GCAP-II is correctly folded by assistance of a factor(s) such as an intra- or intermolecular chaperone. We studied whether a peptide in the pro-leader sequence of the precursor protein (proGCAP-II) contains sufficient information to facilitate the folding of GCAP-II. For this purpose, we prepared proGCAP-II in Escherichia coli by a recombinant technique and examined the disulfide-coupled folding of proGCAP-II from the reduced form. proGCAP-II was quantitatively recovered with the correctly folded structure from the reduced form both in the presence and in the absence of reduced and oxidized glutathione. The protein contains only disulfide linkages at the same positions as the mature form of proGCAP-II, GCAP-II, and the biologically active isomer of GCAP-II in the molecule. These results provide evidence that the propeptide of proGCAP-II is a critical factor in the formation of the correct disulfide paring in the folding of the protein.

Amino Acid Sequence↗
PubMed1998

Automated interpretation of high-energy collision-induced dissociation spectra of singly protonated peptides by 'SeqMS', a software aid for de novo sequencing by tandem mass spectrometry.

SeqMS, a software program designed for the automated interpretation of high-energy collision-induced dissociation (CID) mass spectra of singly protonated peptides ionized by fast atom bombardment, has been developed. The software is capable of probing the sequence of an unknown peptide, and even of certain modified peptides. The program, compiled for WINDOWS95 or NT, also permits the retrieval of raw data and the reconstruction of the spectra on a user-friendly graphical interface with the aid of several tools for processing the spectra, which include setting multiple threshold levels and automatic peak detection. SeqMS is capable of generating candidate sequences, based on the detected peaks, and of displaying the resulting assignments for each candidate in a spectrum or in tabular form. The software has the following capabilities: 1) the ions derived from backbone and side-chain fragmentations, internal and immonium ions, and side-chain loss ions can be used for calculation; 2) 18O-labeling of a peptide at the C terminus, a methodology which was developed to differentiate N-terminal from C-terminal ions, is applicable as an optional setting; 3) modified amino acids and N- or C-terminal blocking groups are taken into account for calculation according to the user's setting in a library; 4) amino acid composition and partial or complete amino acid sequence of a peptide can be used as input for calculation; 5) the assignments of signal output in a spectrum can be graphically edited, and then re-calculated based on the edited peaks. The efficacy of the program is demonstrated by testing 74 high-energy CID spectra, obtained using a four-sector instrument, of synthetic, proteolytic, and biologically active peptides, some of which contain modified groups.

Algorithms↗
PubMed1997

Structure of a covalently cross-linked form of core histones present in the starfish sperm.

The post-translational modification of core histones plays an essential role in chromatin remodeling processes. We recently reported the occurrence of a novel histone modification, involving a epsilon-(gamma-glutamyl)lysine cross-link between a glutamine residue of histone H2B and a lysine residue of histone H4 in the testis of the starfish, Asterina pectinifera[Shimizu, T., Hozumi, K., Horiike, S., Nunomura, K., Ikegami, S., Takao, T., and Shimonishi, Y. (1996) Nature 380, 32]. In order to determine the complete structure of the modified histone heterodimer, p28 from both testis and sperm was purified. p28 was digested with Achromobacter lyticus protease I or Staphylococcus aureus V8 protease to give proteolytic fragments that were separated by HPLC. Amino acid analysis, sequencing, and mass spectrometric analysis of the fragments showed that the amino acid sequences of these fragments are identical to those of both histones H2B and H4, except for two NH2-terminal peptides obtained by digestion with A. lyticus protease I. One of the peptides, K8, was identical to that reported previously, and the other was a here-to-fore unidentified peptide, which was designated K10. Amino acid and positive-ion FAB-MS/MS analyses of K10 showed that it to be a fragment, derived from Gly8-Lys10 of histone H2B and Gly9-Lys16 of histone H4. The yields of K8 and K10 were calculated to be 47 and 42%, respectively, expressed as the percent of the total amount of p28 used in the experiment. Based on these data, the structure of p28 was determined to be a heterodimer, composed of histones H2B and H4, formed through a transglutaminase-catalyzed acyl transfer reaction between Gln9 of histone H2B and Lys5 or Lys12 of histone H4.

Amino Acid Sequence↗
PubMed1997

The oxidation of selenocysteine is involved in the inactivation of glutathione peroxidase by nitric oxide donor.

Glutathione peroxidase (GPx) was inactivated by S-nitroso-N-acetyl-D, L-penicillamine (SNAP), a nitric oxide donor (Asahi, M., Fujii, J., Suzuki, K., Seo, H. G., Kuzuya, T., Hori, M., Tada, M., Fujii, S., and Taniguchi, N. (1995) J. Biol. Chem. 270, 21035-21039). The structural basis of the inactivation was studied. We also show that 3-morpholinosydnonimine N-ethylcarbamide, a peroxynitrite precursor, as well as synthetic peroxynitrite also inactivated bovine GPx. The degree of incorporation of a sulfhydryl reagent, n-octyldithionitrobenzoic acid, into GPx decreased after pretreatment with SNAP as evidenced by mass spectrometry. To identify the modification site of this enzyme by SNAP, both SNAP-pretreated and untreated GPxs were reacted with n-octyldithionitrobenzoic acid and digested with lysylendopeptidase, and the resulting peptides were subjected to mass spectrometry. This technique identified a bridge between two peptides, one of which contains Sec45 at the catalytic center and Cys74, and the other contains Cys91. Although there are two possible combinations, selenocysteine 45 (Sec45) and Cys91 or Cys74 and Cys91, the tertiary structure of GPx indicates that a cross-link between Sec45 and Cys91 is more feasible. This is consistent with the experimental evidence that SNAP specifically inactivates GPx, in which Sec45 forms the catalytic center. Thus, we conclude that SNAP mainly oxidized Sec45 to form a selenenyl sulfide (Se-S) with a free thiol, leading to the inactivation of the enzyme. These data suggest that nitric oxide and its derivatives directly inactivate GPx in a specific manner via the production of a selenenyl sulfide, resulting in an increase in intracellular peroxides that are responsible for cellular damage.

Amino Acid Sequence↗
PubMed1997

Accurate peptide sequencing by post-source decay matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Partial 18O-labeling of peptides has been applied to post-source decay experiments in a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The ions which originate from the carboxyl terminus of a peptide partially retain 18O atoms which have readily been incorporated into the C-terminal carboxyl groups during enzymatic hydrolysis in a buffer containing 40 atom percent H218O. The isotopic resolution of singly charged precursor ions and their product ions obtained for peptides up to ca. 2800 Da has been achieved using the delayed extraction method, which permits the rapid identification and assignment of the 18O-labeled and non-labeled ion species in the PSD spectra. The results obtained from several 18O-labeled peptides, derived from an enzymatic digest, demonstrate the accuracy and reproducibility of the present method, which will be in widespread use for protein identification via database searching or for investigations of totally unknown proteins.

Amino Acid Sequence↗
PubMed1997

Isolation of bioactive compounds from Helix aspersa nerve tissue and the effect of pQPPLPRYamide on heart, esophagus and central neurons of H. aspersa and rectum of Anodonta woodiana.

1. Both acetone and methanol extraction was used to isolate bioactive compounds from 1000 Helix aspersa brains. 2. Seven compounds were isolated of which four were identified as follows: Ha-1, 5-hydroxytryptamine; Ha-3, GSPYFVamide; Ha-4, pQPPLPRYamide; Ha-5, SGYLAFPRMamide. There was insufficient material to identify Ha-2, Ha-6 and Ha-7. 3. Ha-4, pQPPLPRYamide, was found to excite the heart of H. aspersa, relax the esophagus and both excite (mainly) and inhibit central neurons. In addition, this peptide contracted the rectum of Anodonta woodiana. 4. It is concluded that pQPPLPRYamide is an example of a new molluscan peptide family, designated as PRYamide.

Animals↗
PubMed1997

High-sensitivity mass spectrometry for analysis of posttranslational modifications.

Pulsed fast atom bombardment ionization (pulsed-FAB) mass spectrometry has been developed to improve the sensitivity of tandem mass spectrometry (MS/MS), allowing it to be used for the analysis of very small samples. MS/MS, when used with a magnetic four-sector instrument coupled with the pulsed-FAB system, allows significant enhancement in product ion intensity of over ten-fold in magnitude over conventional FAB. MS/MS was applied to the structural analysis of a unique nuclear protein, designated p28, which was isolated from a histone fraction obtained from starfish testes. The results clearly show that protein p28 is a heterodimer composed of testicular histones H2B and H4 which are cross-linked between Gln9 of H2B and Lys5 of H4.

Amino Acid Sequence↗
PubMed1997

Identification of two palmitoyl groups in octopus rhodopsin.

We determined the structure and site of fatty acid incorporated in octopus rhodopsin using a combination of fluorescence label and enzymatic cleavage methods in conjunction with fast-atom bombardment (FAB) mass spectrometry. A single peptide containing two adjacent cysteines, Cys337 and Cys338, was successfully isolated using the fluorescence from a dye conjugated to Cys345. The FAB mass spectrometric analysis of the peptide (323Phe-340Phe) revealed that two palmitoyl groups are linked to Cys337 and Cys338 via thioester bonds in octopus rhodopsin as in bovine rhodopsin.

Amino Acid Sequence↗