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Reilly AM, Cooper RI, Adjiman CS, Bhattacharya S, Boese AD, Brandenburg JG, Bygrave PJ, Bylsma R, Campbell JE, Car R, Case DH, Chadha R, Cole JC, Cosburn K, Cuppen HM, Curtis F, Day GM, DiStasio Jr RA, Dzyabchenko A, van Eijck BP, Elking DM, van den Ende JA, Facelli JC, Ferraro MB, Fusti-Molnar L, Gatsiou CA, Gee TS, de Gelder R, Ghiringhelli LM, Goto H, Grimme S, Guo R, Hofmann DWM, Hoja J, Hylton RK, Iuzzolino L, Jankiewicz W, de Jong DT, Kendrick J, de Klerk NJJ, Ko HY, Kuleshova LN, Li X, Lohani S, Leusen FJJ, Lund AM, Lv J, Ma Y, Marom N, Masunov AE, McCabe P, McMahon DP, Meekes H, Metz MP, Misquitta AJ, Mohamed S, Monserrat B, Needs RJ, Neumann MA, Nyman J, Obata S, Oberhofer H, Oganov AR, Orendt AM, Pagola GI, Pantelides CC, Pickard CJ, Podeszwa R, Price LS, Price SL, Pulido A, Read MG, Reuter K, Schneider E, Schober C, Shields GP, Singh P, Sugden IJ, Szalewicz K, Taylor CR, Tkatchenko A, Tuckerman ME, Vacarro F, Vasileiadis M, Vazquez-Mayagoitia A, Vogt L, Wang Y, Watson RE, de Wijs GA, Yang J, Zhu Q, Groom CR. Report on the sixth blind test of organic crystal structure prediction methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:439-59. [PMID: 27484368 PMCID: PMC4971545 DOI: 10.1107/s2052520616007447] [Citation(s) in RCA: 328] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/04/2016] [Indexed: 05/05/2023]
Abstract
The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.
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Sano K, Tanihara H, Heimark RL, Obata S, Davidson M, St John T, Taketani S, Suzuki S. Protocadherins: a large family of cadherin-related molecules in central nervous system. EMBO J 1993; 12:2249-56. [PMID: 8508762 PMCID: PMC413453 DOI: 10.1002/j.1460-2075.1993.tb05878.x] [Citation(s) in RCA: 279] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Using the polymerase chain reaction, we have isolated numerous rat and human cDNAs of which the deduced amino acid sequences are highly homologous to the sequences of the extracellular domain of cadherins. The entire putative coding sequences for two human proteins defined by two of these cDNAs have been determined. The overall structure of these molecules is very similar to that of classic cadherins, but they have some unique features. The extracellular domains are composed of six or seven subdomains that are very similar to those of cadherins, but have characteristic properties. The cytoplasmic domains, on the other hand, have no significant homology with those of classic cadherins. Since various cDNAs with almost identical features were obtained also from Xenopus, Drosophila and Caenorhabditis elegans, it appears that similar molecules are expressed in a variety of organisms. We have tentatively named these proteins protocadherins. They are highly expressed in brain and their expression appears to be developmentally regulated. The proteins expressed from the two full-length cDNAs in L cells were approximately 170 or 150 kDa in size, and were localized mainly at cell-cell contact sites. Moreover, the transfectants showed cell adhesion activity.
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Koyama T, Obata S, Osabe M, Takeshita A, Yokoyama K, Uchida M, Nishino T, Ogura K. Thermostable farnesyl diphosphate synthase of Bacillus stearothermophilus: molecular cloning, sequence determination, overproduction, and purification. J Biochem 1993; 113:355-63. [PMID: 8486607 DOI: 10.1093/oxfordjournals.jbchem.a124051] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The structural gene for thermostable farnesyl diphosphate synthase from Bacillus stearothermophilus was cloned, sequenced, and overexpressed in Escherichia coli cells. A 1,260-nucleotide sequence of the cloned fragment was determined. This sequence specifies an open reading frame of 891 nucleotides for farnesyl diphosphate synthase. The deduced amino acid sequence shows a 42% similarity with that of E. coli FPP synthase [Fujisaki et al. (1990) J. Biochem. 108, 995-1000]. Comparison with prenyltransferases from a wide range of organisms, from bacteria to human, revealed the presence of seven highly conserved regions. In contrast to thermolabile prenyltransferases, which have four to six cysteine residues, the thermostable farnesyl diphosphate synthase carries only two cysteine residues. This enzyme is also unique in that some of the amino acids that are fully conserved in equivalents from other sources are replaced by functionally different amino acids. Construction of an overproducing strain provided a sufficient supply of this enzyme and it was purified to homogeneity. The purified recombinant enzyme is immunochemically identical with the native B. stearothermophilus enzyme, and it is not inactivated even after treatment at 65 degrees C for 70 min.
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Obata S, Sago H, Mori N, Rochelle JM, Seldin MF, Davidson M, St John T, Taketani S, Suzuki ST. Protocadherin Pcdh2 shows properties similar to, but distinct from, those of classical cadherins. J Cell Sci 1995; 108 ( Pt 12):3765-73. [PMID: 8719883 DOI: 10.1242/jcs.108.12.3765] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell adhesion and several other properties of a recently identified cadherin-related protein, protocadherin Pcdh2, were characterized. A chimeric Pcdh2 in which the original cytoplasmic domain was replaced with the cytoplasmic domain of E-cadherin was expressed in mouse L cells. The expressed protein had a molecular mass of about 150 kDa and was localized predominantly at the cell periphery, as was the wild-type Pcdh2. In a conventional cell aggregation assay, the transfectants showed cell aggregation activity comparable to that of classical cadherins. This activity was Ca(2+)-dependent and was inhibited by the addition of anti-Pcdh2 antibody, indicating that the chimeric Pcdh2, and probably the wild-type Pcdh2, has Ca(2+)-dependent cell aggregation activity. Mixed cell aggregation assay using L cells and different types of transfectants showed that the activity of Pcdh2 was homophilic and molecular type specific and that Pcdh2 was transfectants did not aggregate with other types of transfectants or with L cells. In immunoprecipitation, the chimeric Pcdh2 co-precipitated with a 105 kDa and a 95 kDa protein, whereas wild-type Pcdh2 co-precipitated with no major protein. Pcdh2 was easily solubilized with non-ionic detergent, in contrast to the case of classical cadherins. On immunofluorescence microscopy, the somas of Purkinje cells were diffusely stained with anti-human Pcdh2 antibody. Mouse Pcdh1 and Pcdh2 were mapped to a small segment of chromosome 18, suggesting that various protocadherins form a gene cluster at this region. The present results suggest that Pcdh2, and possibly other protocadherins as well as protocadherin-related proteins such as Drosophila fat, mediate Ca(2+)-dependent and specific homophilic cell-cell interaction in vivo and play an important role in cell adhesion, cell recognition, and/or some other basic cell processes.
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Obata S, Usukura J. Morphogenesis of the photoreceptor outer segment during postnatal development in the mouse (BALB/c) retina. Cell Tissue Res 1992; 269:39-48. [PMID: 1423483 DOI: 10.1007/bf00384724] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Disc formation of rod photoreceptor cells in developing BALB/c mice retinas was studied by rapid freeze, freeze-substitution, freeze-etching, immunocytochemistry, and myosin S-1 decoration methods. Freeze-substituted photoreceptor cells contained variously shaped vesicles in the apical swelling of the connecting cilium or the base of the outer segment during postnatal development. Rapid freezing successfully arrested pinocytosis; the fusion of small vesicles to give large ones, and the compression of certain vesicles (0.3-0.6 micron) appears to lead gradually to the formation of the so-called discs. We therefore propose that membranous discs are formed by the fusion of small pinocytotic vesicles and their subsequent compression. Discs formed in this way were partially stacked, but were ordered at random during the early developmental stages. During development, a partial stack of discs was progressively rearranged to a regular form as seen in mature outer segments. Cytoskeletal actin was expected to be involved in the disc formation; it was demonstrated in the distal axoneme of the connecting cilium during development and showed no change in its distribution. However, the polarity of the actin filaments, as revealed by myosin S-1 decoration in early developmental stages, was much more variable than in the adult. Barbed ends of actin filaments were associated with the plasma membrane or the membrane of vesicles. We also found actin filaments coiled up helically on ciliary microtubules.
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Tanihara H, Kido M, Obata S, Heimark RL, Davidson M, St John T, Suzuki S. Characterization of cadherin-4 and cadherin-5 reveals new aspects of cadherins. J Cell Sci 1994; 107 ( Pt 6):1697-704. [PMID: 7962210 DOI: 10.1242/jcs.107.6.1697] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Several properties of cadherin-4 and cadherin-5 were characterized by using the cDNA transfection approach. The proteins of both cadherins had a relative molecular mass of about 130 kDa and were present at the cell periphery, especially at cell-cell contact sites. These cadherins were easily digested with trypsin, and Ca2+ protected cadherin-4, but not cadherin-5, from the digestion. In immunoprecipitation, cadherin-4 co-precipitated with two major proteins of 105 kDa and 95 kDa, respectively. The 105 kDa and the 95 kDa proteins are likely to correspond to alpha- and beta-catenins. Cadherin-5 co-precipitated with only one major protein of 95 kDa, but seems to associate with the 105 kDa protein. On the other hand, plakoglobin or gamma-catenin did not co-precipitate well with either cadherin-4 or cadherin-5 in immunoprecipitation, but plakoglobin also appears to associated weakly with these cadherins. Cadherin-4 transfectants aggregated within 30 minutes in a cell aggregation assay, but cadherin-5 transfectants did not aggregate under the same conditions. Furthermore, the transfectants of chimeric cadherin-4 with cadherin-5 cytoplasmic domain showed cell aggregation activity comparable to that of wild-type cadherin-4 transfectants, whereas the transfectants of chimeric cadherin-5 with cadherin-4 cytoplasmic domain did not show appreciable cell aggregation, suggesting that the extracellular domains of cadherins, in conjunction with their cytoplasmic domains, play an important role in cell aggregation activity. These results show that cadherin-4 is very similar to the classical cadherins, whereas cadherin-5 is functionally as well as structurally distinct from classical cadherins.
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Koyama T, Tajima M, Sano H, Doi T, Koike-Takeshita A, Obata S, Nishino T, Ogura K. Identification of significant residues in the substrate binding site of Bacillus stearothermophilus farnesyl diphosphate synthase. Biochemistry 1996; 35:9533-8. [PMID: 8755734 DOI: 10.1021/bi960137v] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Farnesyl diphosphate synthases have been shown to possess seven highly conserved regions (I-VII) in their amino acid sequences [Koyama et al. (1993) J. Biochem. (Tokyo) 113, 355-363]. Site-directed mutants of farnesyl diphosphate synthase from Bacillus stearothermophilus were made to evaluate the roles of the conserved aspartic acids in region VI and lysines in regions I, V, and VI. The aspartate at position 224 was changed to alanine or glutamate (mutants designated as D224A and D224E, respectively); aspartates at positions 225 and 228 were changed to isoleucine and alanine (D225I, D228A); lysine at position 238 was changed to either alanine or arginine (K238A, K238R). The lysines at positions 47 and 183 were changed to isoleucine and alanine (K471, K183A), respectively. Kinetic analyses of the wild-type and mutant enzymes indicated that the mutagenesis of Asp-224 and Asp-225 resulted in a decrease of Kcat values of approximately 10(4)- to 10(5)-fold compared to the wild type. On the other hand, D228A showed a Kcat value approximately one-tenth of that of the wild type, and the k(m) value for isopentenyl diphosphate increased approximately 10-fold. Both K471 and K183A showed k(m) values for isopentenyl diphosphate 20-fold larger and kcat values 70-fold smaller than the wild type. These results suggest that the two conserved lysines in regions I and V contribute to the binding of isopentenyl diphosphate and that the first and the second aspartates in region VI are involved in catalytic function. Aspartate-228 is also important for the binding of isopentenyl diphosphate rather than for catalytic reaction.
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Koike-Takeshita A, Koyama T, Obata S, Ogura K. Molecular cloning and nucleotide sequences of the genes for two essential proteins constituting a novel enzyme system for heptaprenyl diphosphate synthesis. J Biol Chem 1995; 270:18396-400. [PMID: 7629164 DOI: 10.1074/jbc.270.31.18396] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The genes encoding two dissociable components essential for Bacillus stearothermophilus heptaprenyl diphosphate synthase (all-trans-hexparenyl-diphosphate:isopentenyl-diphosphate hexaprenyl-trans-transferase, EC 2.5.1.30) were cloned, and their nucleotide sequences were determined. Sequence analyses revealed the presence of three open reading frames within 2,350 base pairs, designated as ORF-1, ORF-2, and ORF-3 in order of nucleotide sequence, which encode proteins of 220, 234, and 323 amino acids, respectively. Deletion experiments have shown that expression of the enzymatic activity requires the presence of ORF-1 and ORF-3, but ORF-2 is not essential. As a result, this enzyme was proved genetically to consist of two different protein compounds with molecular masses of 25 kDa (Component I) and 36 kDa (Component II), encoded by two of the three tandem genes. The protein encoded by ORF-1 has no similarity to any protein so far registered. However, the protein encoded by ORF-3 shows a 32% similarity to the farnesyl diphosphate synthase of the same bacterium and has seven highly conserved regions that have been shown typical in prenyltransferases (Koyama, T., Obata, S., Osabe, M., Takeshita, A., Yokoyama, K., Uchida, M., Nishino, T., and Ogura, K. (1993) J. Biochem. (Tokyo) 113, 355-363).
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Sago H, Kitagawa M, Obata S, Mori N, Taketani S, Rochelle JM, Seldin MF, Davidson M, St John T, Suzuki ST. Cloning, expression, and chromosomal localization of a novel cadherin-related protein, protocadherin-3. Genomics 1995; 29:631-40. [PMID: 8575755 DOI: 10.1006/geno.1995.9956] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To study the diversity of the protocadherin family, the cDNA clones for a novel protocadherin were isolated by screening rat brain cDNA libraries with a cDNA fragment obtained by PCR, and some of the properties were then characterized. The overall structure of the protein defined by the clone is similar to that of previously identified protocadherins; however, the cytoplasmic domain is distinct from those of previously cloned protocadherins or any other protein sequences in the data bank. We named this protocad herin-3 (Pcdh3) since this is the third protocadherin of which the entire coding sequence has been determined. Most of the deduced amino acid sequences of other cDNA clones obtained by the screening show high homology with but are distinct from that of Pcdh3, indicating that most of these sequences correspond to homologous but different protocadherins. These results demonstrate that Pcdh3 and the protocadherins defined by these clones constitute a protocadherin subfamily. Chromosome mapping indicates that mouse Pcdh3 is located in a specific region of mouse chromosome 18, close to the location of previously cloned protocadherins, suggesting that various protocadherins form a cluster in this region. In situ hybridization results showed that Pcdh3 and its related proteins were expressed at various areas in brain. The expressed Pcdh3 protein from the cDNA in mouse L cells was about 100 kDa in molecular weight and was localized at cell-cell contact sites. In contrast to the classical cadherins, however, the expressed Pcdh3 was sensitive to trypsin even in the presence of Ca2+, and the transfectants did not show strong Ca(2+)-dependent cell aggregation activity. These results indicate the structural and possibly functional diversity of the protocadherin family and suggest a distinctive biological role for Pcdh3.
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Takeda H, Matsunaga N, Sakamoto I, Obata S, Nakamura S, Hayashi K. Spontaneous dissection of the celiac and hepatic arteries treated by transcatheter embolization. AJR Am J Roentgenol 1995; 165:1288-9. [PMID: 7572520 DOI: 10.2214/ajr.165.5.7572520] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Case Reports |
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Obata S, Obata J, Das A, Gilbert CD. Molecular correlates of topographic reorganization in primary visual cortex following retinal lesions. Cereb Cortex 1999; 9:238-48. [PMID: 10355904 DOI: 10.1093/cercor/9.3.238] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adult visual cortex undergoes substantial functional change as a result of alterations in visual experience. Binocular retinal lesions lead to a reorganization of the visuotopic map in primary visual cortex. Associated with this change is a strengthening of an existing plexus of long-range horizontal connections by sprouting of axon collaterals and synaptogenesis. To explore the molecular substrate of this change, we studied the expression of potential factors involved in neural plasticity in the area of reorganization. We found elevation in a number of factors as early as 3 days following the lesion, including neurotrophins BDNF, NT3, NGF and the insulin-like growth factor IGF-1. Associated with the changes in neurotrophin levels was an elevation in their receptors. We also measured elevation of transcription factors, CaMKII, MAP2 and synapsins. These experiments provide evidence for a signal transduction cascade associated with cortical reorganization.
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Obata S, Sago H, Mori N, Davidson M, St John T, Suzuki ST. A common protocadherin tail: multiple protocadherins share the same sequence in their cytoplasmic domains and are expressed in different regions of brain. CELL ADHESION AND COMMUNICATION 1998; 6:323-33. [PMID: 9865466 DOI: 10.3109/15419069809010791] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To study the diversity of protocadherins, a rat brain cDNA library was screened using a cDNA for the cytoplasmic domain of human protocadherin Pcdh2 as a probe. The resultant clones contained three different types. One type corresponds to rat Pcdh2; the other two types are distinct from Pcdh2 but contain the same sequence in their cytoplasmic domains and part of the 3' flanking sequence. To clarify the structure of the proteins defined by the new clones, a putative entire coding sequence corresponding to one of the clones was determined. The overall structure is essentially the same as Pcdh2, indicating that the proteins defined by this clone, and probably by other clones, belong to the protocadherin family. Two PCR experiments and an RNase protection assay showed the existence of the corresponding mRNAs in rat brain preparations. Human and mouse cDNA clones with the same sequence properties were also isolated. Taken together, these results indicate that the clones are not cloning artifacts and that corresponding mRNAs are actually expressed in brains of various species. The results of in situ hybridization showed that the mRNAs corresponding to these clones were expressed in different regions in brain. Since protocadherins encoded by these mRNAs are likely to have different specificity in their interaction and share a common activity at their cytoplasmic domains, these protocadherins may provide a molecular basis, in part, to support the complex cell cell interaction in brain.
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Comparative Study |
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Obata S, Taguchi S, Kumagai I, Miura K. Molecular cloning and nucleotide sequence determination of gene encoding Streptomyces subtilisin inhibitor (SSI). J Biochem 1989; 105:367-71. [PMID: 2732212 DOI: 10.1093/oxfordjournals.jbchem.a122670] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A gene for Streptomyces subtilisin inhibitor (SSI) from Streptomyces albogriseolus S-3253 was cloned into E. coli plasmid pBR322 using two oligodeoxyribonucleotides corresponding to Asp68 to Pro77 and Asn99 to Gly107 of the protein, respectively. The SSI gene was localized on a 1.8-kbp BglII/SalI fragment. The nucleotide sequence of this 1.8-kbp fragment was determined by the dideoxy sequencing method. The amino acid sequence of the mature SSI coding region derived from the nucleotide sequence determination corresponded exactly to that from protein sequencing analysis. The nucleotide sequence analysis showed the presence of a putative signal peptide comprising 31 amino acids preceding the mature SSI region. The major transcriptional start point was identified to be 60 nucleotides upstream from the putative initiation codon for translation by the primer extension method. The -45 to -25 region upstream from transcriptional start point was quite homologous to that of CTC promoter of Bacillus subtilis. The overall G + C content of this 1.8-kbp fragment was 72%. On the other hand, an extremely high G + C content (96%) was found at the third letter of codons in the SSI coding region.
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Obata S, Shimoi Y. Control of molecular orientations of poly(3-hexylthiophene) on self-assembled monolayers: molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:9265-70. [DOI: 10.1039/c3cp44150d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ohto C, Ishida C, Nakane H, Muramatsu M, Nishino T, Obata S. A thermophilic cyanobacterium Synechococcus elongatus has three different Class I prenyltransferase genes. PLANT MOLECULAR BIOLOGY 1999; 40:307-21. [PMID: 10412909 DOI: 10.1023/a:1006295705142] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Prenyltransferases (prenyl diphosphate synthases), which are a broad group of enzymes that catalyze the consecutive condensation of homoallylic diphosphate of isopentenyl diphosphates (IPP, C5) with allylic diphosphates to synthesize prenyl diphosphates of various chain lengths, have highly conserved regions in their amino acid sequences. Based on the above information, three prenyltransferase homologue genes were cloned from a thermophilic cyanobacterium, Synechococcus elongatus. Through analyses of the reaction products of the enzymes encoded by these genes, it was revealed that one encodes a thermolabile geranylgeranyl (C20) diphosphate synthase, another encodes a farnesyl (C15) diphosphate synthase whose optimal reaction temperature is 60 degrees C, and the third one encodes a prenyltransferase whose optimal reaction temperature is 75 degrees C. The last enzyme could catalyze the synthesis of five prenyl diphosphates of farnesyl, geranylgeranyl, geranylfarnesyl (C25), hexaprenyl (C30), and heptaprenyl (C35) diphosphates from dimethylallyl (C5) diphosphate, geranyl (C10) diphosphate, or farnesyl diphosphate as the allylic substrates. The product specificity of this novel kind of enzyme varied according to the ratio of the allylic and homoallylic substrates. The situations of these three S. elongatus enzymes in a phylogenetic tree of prenyltransferases are discussed in comparison with a mesophilic cyanobacterium of Synechocystis PCC6803, whose complete genome has been reported by Kaneko et al. (1996).
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Matsuo S, Yamaguchi S, Miyamoto S, Ishii T, Tsuneoka N, Obata S, Hayashi T, Kanematsu T. Ruptured aneurysm of the visceral artery: report of two cases. Surg Today 2002; 31:660-4. [PMID: 11495164 DOI: 10.1007/s005950170103] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We present herein two cases of a ruptured aneurysm of the visceral artery. The first case involved a 74-year-old man with abdominal pain who was admitted to our hospital with a tentative diagnosis of intra-abdominal bleeding of unknown origin. Computed tomography revealed a hematoma in the greater curvature of the stomach. At surgery, a hematoma along the right gastroepiploic artery was found and totally removed. Histological examination showed a pseudo-aneurysm of unknown etiology. The second case involved a 68-year-old man with progressive anemia who presented with spontaneous intra-abdominal bleeding. A ruptured aneurysm of the accessory middle colic artery was diagnosed by superior mesenteric angiography. The ruptured aneurysm was ligated and totally resected without a colectomy. Histological examination showed a pseudoaneurysm of unknown etiology. The postoperative courses were uneventful, and both patients were doing well at the time of writing.
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Case Reports |
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Obata S, Suenaga M, Araki K, Fujioka Y, Kimura K, Maeda K, Miura K, Mizutani J. Use of strip biopsy in a case of early duodenal cancer. Endoscopy 1992; 24:232-4. [PMID: 1587243 DOI: 10.1055/s-2007-1010470] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In a 67-year-old man referred for investigation of an abdominal mass, upper gastrointestinal endoscopy incidentally revealed a polypoid lesion with a central depression in the duodenum. The abdominal mass causing gastric compression was shown by ultrasonography and CT scan to be cyst anterior to the pancreas. Biopsy of the duodenal lesion, however, was suggestive of carcinoma. Strip biopsy was therefore performed. Histological examination showed a tubular adenocarcinoma with invasion limited to the mucosa, and indicated that complete endoscopic resection had been achieved. Follow-up over ten months did not reveal recurrence of the tumor. Strip biopsy would appear to be a safe and efficient method for management of early gastrointestinal tract cancer also in the duodenum.
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Case Reports |
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Kajino T, Ohto C, Muramatsu M, Obata S, Udaka S, Yamada Y, Takahashi H. A protein disulfide isomerase gene fusion expression system that increases the extracellular productivity of Bacillus brevis. Appl Environ Microbiol 2000; 66:638-42. [PMID: 10653729 PMCID: PMC91874 DOI: 10.1128/aem.66.2.638-642.2000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a versatile Bacillus brevis expression and secretion system based on the use of fungal protein disulfide isomerase (PDI) as a gene fusion partner. Fusion with PDI increased the extracellular production of heterologous proteins (light chain of immunoglobulin G, 8-fold; geranylgeranyl pyrophosphate synthase, 12-fold). Linkage to PDI prevented the aggregation of the secreted proteins, resulting in high-level accumulation of fusion proteins in soluble and biologically active forms. We also show that the disulfide isomerase activity of PDI in a fusion protein is responsible for the suppression of the aggregation of the protein with intradisulfide, whereas aggregation of the protein without intradisulfide was prevented even when the protein was fused to a mutant PDI whose two active sites were disrupted, suggesting that another PDI function, such as chaperone-like activity, synergistically prevented the aggregation of heterologous proteins in the PDI fusion expression system.
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Kojima S, Obata S, Kumagai I, Miura K. Alteration of the Specificity of the Streptomyces Subtilisin Inhibitor by Gene Engineering. Nat Biotechnol 1990; 8:449-52. [PMID: 1366538 DOI: 10.1038/nbt0590-449] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have altered the amino acid at the center of the reactive site (methionine 73) of Streptomyces subtilisin inhibitor (SSI) by site-directed and cassette mutagenesis. Replacement by lysine or arginine resulted in trypsin inhibitory activity, replacement only by lysine gave inhibition of lysyl endopeptidase, and replacement by tyrosine or tryptophan resulted in inhibition of alpha-chymotrypsin. The four mutant SSIs retained their native activity against subtilisin BPN'. Thus by altering only one amino acid residue at the reactive site of SSI to the substrate specificity of the respective protease we could successfully change its inhibitory profile.
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Hirayama T, Ishida C, Kuromori T, Obata S, Shimoda C, Yamamoto M, Shinozaki K, Ohto C. Functional cloning of a cDNA encoding Mei2-like protein from Arabidopsis thaliana using a fission yeast pheromone receptor deficient mutant. FEBS Lett 1997; 413:16-20. [PMID: 9287109 DOI: 10.1016/s0014-5793(97)00871-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
To isolate Arabidopsis cDNAs that encode signal transducers and components involved in the regulation of meiosis, a trans-complementation analysis was performed using a Schizosaccharomyces pombe meiosis-defective mutant in which the genes for pheromone receptors were disabled. One cDNA obtained in this screening encodes a polypeptide, named AML1, that shows significant similarity to S. pombe Mei2 protein and has three putative RNA-recognition motifs like as Mei2. Mei2 is involved in the regulation of meiosis in fission yeast. Northern blot analysis showed that the AML1 gene is expressed in each organ. The possible functions of AML1 are discussed.
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Obata S, Furukubo S, Kumagai I, Takahashi H, Miura K. High-level expression in Streptomyces lividans 66 of a gene encoding Streptomyces subtilisin inhibitor from Streptomyces albogriseolus S-3253. J Biochem 1989; 105:372-6. [PMID: 2659584 DOI: 10.1093/oxfordjournals.jbchem.a122671] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A secretory expression system for Streptomyces subtilisin inhibitor (SSI) was established in a heterologous host, Streptomyces lividans 66, by introducing the 1.8-kbp BglII/SalI fragment containing SSI gene into the Streptomyces multicopy vector, pIJ 702. The expression of SSI did not depend on the orientation of the 1.8-kbp BglII/SalI fragment or on the promoter for tyrosinase gene (mel) in pIJ 702, which suggested that this fragment also carries the SSI promoter. The expressed SSI in S.lividans 66 was secreted into the culture medium in a large amount, as observed with the original strain, S. albogriseolus S-3253. Amino acid sequence analysis showed that the SSI secreted from S. lividans 66 contained three additional amino acid residues in the NH2-terminal region. The inhibitory activity toward subtilisin BPN' and the antigenic activity of the SSI secreted from S. lividans 66 were found to be identical with those of authentic SSI.
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Koyama T, Obata S, Saito K, Takeshita-Koike A, Ogura K. Structural and functional roles of the cysteine residues of Bacillus stearothermophilus farnesyl diphosphate synthase. Biochemistry 1994; 33:12644-8. [PMID: 7918490 DOI: 10.1021/bi00208a015] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
p-(Chloromercuri)benzoic acid inhibited the catalytic activity of Bacillus stearothermophilus farnesyl diphosphate synthase (FPP synthase), which contains only two cysteine residues at positions 73 and 289. In order to explore the role of the cysteine residues, either or both of them were replaced with phenylalanine or serine. Five mutant enzymes, C73F, C73S, C289F, C289S, and C73S-C289S, were overproduced in Escherichia coli and purified to homogeneity. All of them were active as farnesyl diphosphate synthase, showing specific activities comparable to that of the wild-type enzyme. These results indicate that neither of the cysteines is essential for catalytic function. The C73F mutant, however, was very sensitive to heat treatment, while C73S was as highly stable as the wild type. The Km value of C289F for isopentenyl diphosphate is 10 times that of the wild type. The wild-type enzyme was converted into an oxidized form which was separable from the native enzyme on ion-exchange chromatography, and this conversion was accelerated by cupric ions. Similar conversion has previously been reported by several researchers, who found the occurrence of two forms of pig liver FPP synthase and who attributed this phenomenon to the oxidoreduction of sulfhydryl and disulfide groups. However, even the C73S-C289S mutant, which has no cysteine residues, was also converted into an oxidized form as in the case of the wild-type enzyme. These results provide evidence that residues other than cysteine are involved in the conversion of this enzyme into the oxidized form.
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Fujihisa H, Honda K, Obata S, Yamawaki H, Takeya S, Gotoh Y, Matsunaga T. Crystal structure of anhydrous 5-aminotetrazole and its high-pressure behavior. CrystEngComm 2011. [DOI: 10.1039/c0ce00278j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Obata S. The influence of aphids on the behaviour of adults of the ladybird beetle,Harmonia axyridis (Col.: Coccinellidae). ACTA ACUST UNITED AC 1997. [DOI: 10.1007/bf02769885] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Qi Z, Murase K, Obata S, Sokabe M. Extracellular ATP-dependent activation of plasma membrane Ca(2+) pump in HEK-293 cells. Br J Pharmacol 2000; 131:370-4. [PMID: 10991933 PMCID: PMC1572318 DOI: 10.1038/sj.bjp.0703563] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
1. It is well known that extracellular ATP (ATP(o)) elevates the intracellular Ca(2+) concentration ([Ca(2+)](i)) by inducing Ca(2+) influx or mobilizing Ca(2+) from internal stores via activation of purinoceptors in the plasma membrane. This study shows that ATP(o) also activates the plasma membrane Ca(2+) pumps (PMCPs) to bring the elevated [Ca(2+)](i) back to the resting level in human embryonic kidney-293 (HEK-293) cells. 2. The duration of ATP(o)-induced intracellular Ca(2+) transients was significantly increased by PMCP blockers, La(3+) or orthovanadate. In contrast, replacement of extracellular Na(+) with NMDG(+), a membrane-impermeable cation, had no significant effect on duration, thus suggesting that Na(+)/Ca(2+) exchangers do not participate in the ATP(o)-induced Ca(2+) transient. 3. A rapid and significant decrease in [Ca(2+)](i), which was not dependent on extracellular Na(+), was induced by ATP(o) in cells pretreated with thapsigargin (TG). This decrease was blocked by orthovanadate, indicating that it was caused by PMCPs rather than sarco/endoplasmic reticulum Ca(2+) pumps (SERCPs). 4. UTP and ATPgammaS also caused a decrease in [Ca(2+)](i) in cells pretreated with TG, although they were less effective than ATP. The effect of UTP implies the involvement of both P2Y(1) and P2Y(2) receptors, while the effect of ATPgammaS implies no significant role of ectophosphorylation and agonist hydrolysis in the agonist-induced [Ca(2+)](i) decreases. 5. These results point to a role of PMCPs in shaping the Ca(2+) signal and in restoring the resting [Ca(2+)](i) level to maintain intracellular Ca(2+) homeostasis after agonist stimulation.
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